- beg-bogas@psb.ugent.be - maillist.psb.ugent.be

[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by Lieven Sterck 17 Nov '07

17 Nov '07

Hi Marek, The artemini tools works again on these two loci. We're still looking into the Esi0000_0141 record, why it doesn't save. grtz, lieven > Hi Lieven,, > I am deeply sorry, but two more problems emerged: > > 1. The Artemini tool fails to open for the following two models: > Esi0065_0017 and Esi0080_0048. After clicking on the "Modify using > Artemini" the Artemini starts to load but it stops with an error > message "The application encountered an unforseen error" > > 2. I tried several times to save the description of the Esi0000_0141 > gene, but the text filled into the "Short name" and "Definition" > fields always failed to be saved and the edit was not recorded in the > list of my 5 most recent annotations at the home page. > > Could you, pease, look also on these troubles? > Thanks, > Marek > > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> Hi Marek, >> >> sorry for that! >> We'll look into it. >> >> thanks, >> lieven >> >> >>> Hi Lieven, >>> >>> I am working hard on the annotation but unfortunatelly still some >>> unexpected problems emerge. Now I face a trouble with annotating the >>> gene Esi0030_0124. When I insert the correct coordinates, which are as >>> follows: >>> >>> 570185..570280,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 >>> >>> However, after I try to save the change to the server, the program >>> replies with an error message, and when I open the window with the >>> coordinates, they are changed so that they look like this: >>> >>> 2,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 >>> >>> I have not seen this behaviour with other genes, so I have no >>> explanation for it. What is going on? >>> >>> Thanks, >>> Marek >>> >>> >>> >>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>> >>>> Hi Marek, >>>> >>>> This is a not so easy issue (for us! not for you). >>>> the best option would be to select the model labeled 'CDS' and then >>>> insert >>>> your new coordinates. The other models you can ignore. >>>> >>>> grtz, >>>> lieven >>>> >>>>> Hi Lieven, >>>>> >>>>> thanks for the comments, it now seems that he problem with saving the >>>>> changes of gene models has been solved. I am sorry, however, to say >>>>> that I have just encountered another point requiring a discussion >>>>> with >>>>> you. I found that some genes I am annotating are incorrectly >>>>> predicted >>>>> as two or even three independent loci. How to correct these >>>>> instances? >>>>> Should I merge somehow the models into one, which I subsequetly >>>>> modify >>>>> bu inserting correct coordinates? If yes, how should I do it? Or >>>>> should I simply insert the correct coordinates into a field of one of >>>>> the partial "submodels" and ignore or delete the remaining? >>>>> Thanks, >>>>> Marek >>>>> >>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>> >>>>>> Hi Marek, >>>>>> >>>>>> I spotted the problem. You are talking about locus Esi0425_0013, no? >>>>>> I can see that you made an edit in the DB, but the problem is that >>>>>> there >>>>>> seems to be a double save. If you check in the history the last-1 >>>>>> date >>>>>> you'll see your edit. >>>>>> >>>>>> We are sorting this out as quickly as possible. >>>>>> >>>>>> best regards, >>>>>> lieven >>>>>> >>>>>> >>>>>>> Dear Lieven, >>>>>>> >>>>>>> thanks for the change in artemini, this is exactly what I think >>>>>>> will >>>>>>> make the annotation much more straightforward. I checked the system >>>>>>> with one gene (correcting coordinates of one exon). I saved the >>>>>>> modified coordinates using "Save to server" command in "File" menu >>>>>>> option, but the model has not changed in the database yet. Are you >>>>>>> reviewing opur annotations before incorporating them into the >>>>>>> database? Or what is going on? >>>>>>> Thanks. Cheers, >>>>>>> >>>>>>> Marek >>>>>>> >>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> we made some adjustments to the artemini functionality and as a >>>>>>>> result >>>>>>>> the >>>>>>>> coordinates you see in the artemini window are now the same as in >>>>>>>> the >>>>>>>> webpage (= they are in reference to the whole scaffold). >>>>>>>> You can just copy and paste your coordinates into the artemini, >>>>>>>> save >>>>>>>> it >>>>>>>> and they will be entered into the DB. >>>>>>>> >>>>>>>> I hope this can satisfy your needs. If not, please do let me know, >>>>>>>> so >>>>>>>> we >>>>>>>> can think of better solution. >>>>>>>> >>>>>>>> thanks and best regards, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: Re: Ectocarpus proteins >>>>>>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>>>>>> Date: Thu, November 8, 2007 11:17 pm >>>>>>>> To: melias(a)natur.cuni.cz >>>>>>>> Cc: cock(a)sb-roscoff.fr >>>>>>>> beg-bogas(a)psb.ugent.be >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> You can find a manual on how to use the artemis tool on the Sanger >>>>>>>> Institute website. >>>>>>>> May I inquire if you find the artemis tool itself not >>>>>>>> user-friendly >>>>>>>> or >>>>>>>> rather the way it is incoporated in the portal? >>>>>>>> >>>>>>>> The coordinates in the artemini view differ indeed from the ones >>>>>>>> on >>>>>>>> the >>>>>>>> webpage. this is because the sequence you get to see in the >>>>>>>> artemini >>>>>>>> view >>>>>>>> is only a subpart of the whole scaffold (this in order to let the >>>>>>>> procedure go faster). The coordinates you see in artemini are in >>>>>>>> reference >>>>>>>> to the subpart while you have (and also on the webpage) them in >>>>>>>> reference >>>>>>>> of the whole scaffold. >>>>>>>> >>>>>>>> In theory it is possible to make the coordinates 'box' editable. >>>>>>>> but, >>>>>>>> ... >>>>>>>> i'm a little bit reluctant to do this due to bad experience with >>>>>>>> this >>>>>>>> approach in previous projects. We noticied it is very easy to >>>>>>>> include >>>>>>>> mistakes this way (aspecially for non experienced annotators). >>>>>>>> That >>>>>>>> is >>>>>>>> why >>>>>>>> we include the artemini system in this version (where some basic >>>>>>>> checks >>>>>>>> on >>>>>>>> the structure are performed and you have the visual check of the >>>>>>>> structure). >>>>>>>> But I also completely understand your point that for more >>>>>>>> experienced >>>>>>>> users this might not be ideal... >>>>>>>> What we also can do is to add a function in the artemini to >>>>>>>> 'transfer' >>>>>>>> the >>>>>>>> coordinates you enter (in reference of the whole scaffold) onto >>>>>>>> the >>>>>>>> subpart in artemini. That way you could just paste your >>>>>>>> coordinates >>>>>>>> into >>>>>>>> the coordinate box of artemini, push the 'transfer' button and >>>>>>>> they >>>>>>>> will >>>>>>>> be adjusted onto the subpart. You can then also profit from the >>>>>>>> visual >>>>>>>> check. When you then save your modifications they will be entered >>>>>>>> to >>>>>>>> the >>>>>>>> DB. >>>>>>>> Do you think this might be more useful? or does it still sounds to >>>>>>>> much >>>>>>>> of >>>>>>>> a hastle? >>>>>>>> >>>>>>>> best and thanks for the feedback, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>>> Dear Lieven, >>>>>>>>> >>>>>>>>> thanks for the link, I have successfully downloaded the protein >>>>>>>>> database. I would like to start making corrections of the gene >>>>>>>>> models >>>>>>>>> I >>>>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is >>>>>>>> there >>>>>>>> any >>>>>>>> manual how to work with the Artemini tool? I found it not be too >>>>>>>> user-friendly. For instance, I do not understand why the exon >>>>>>>> coordinates indicated by Artemini differs from the actual >>>>>>>> coordinates >>>>>>>> on >>>>>>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>>>>>> coordinates, with an incorrect first exon, are as follows: >>>>>>>>> >>>>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> I would like to change the first exon so that the coordinates are >>>>>>>>> like >>>>>>>> this: >>>>>>>>> >>>>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> The coordinates given for this gene in Artemini are as follows: >>>>>>>>> >>>>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>>>>>> >>>>>>>>> Why there is the difference? I have to say that I would highly >>>>>>>>> appreciate if it is possible to edit gene models just by typing >>>>>>>>> the >>>>>>>> correct coordinates of exons I found by comparing my CDS models >>>>>>>> with >>>>>>>> the >>>>>>>> contig sequence. Is this possible? >>>>>>>>> Thank you and best regards, >>>>>>>>> >>>>>>>>> Marek E. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>> >>>>>>>>>> Dear Marek, >>>>>>>>>> the download is available from this address: >>>>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>>>>>> (login/passw : psbguest/ectocarpus) >>>>>>>>>> Apologises that I haven't informed you earlier, it is quite >>>>>>>>>> hectic >>>>>>>>>> for >>>>>>>> the >>>>>>>>>> moment. >>>>>>>>>> please let me know if this doesn't work. >>>>>>>>>> best regards, >>>>>>>>>> lieven >>>>>>>>>>> Dear Lieven, >>>>>>>>>>> you mentioned that from this week's Monday the whole predicted >>>>>>>> proteome of Ectocarpus should be available for download. I tried >>>>>>>> to >>>>>>>> find >>>>>>>> a >>>>>>>> link to the file at BOGAS web page but haven't found any. Could >>>>>>>> you, >>>>>>>> please, let me know, where to go for the downloading? >>>>>>>>>>> Thanks, best regards, >>>>>>>>>>> Marek Elias >>>>>>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>>>> Dear Marek, >>>>>>>>>>>> From monday on you will be able to download all predicted >>>>>>>>>>>> protein/genes >>>>>>>>>>>> in batch. >>>>>>>>>>>> sorry for the delay. >>>>>>>>>>>> regards, >>>>>>>>>>>> lieven >>>>>>>>>>>> Kenny Billiau wrote: >>>>>>>>>>>>> -------- Original Message -------- >>>>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>>>>>> References: >>>>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>>>>>> Hi Kenny, >>>>>>>>>>>>> thanks for the advice with getting the access to the >>>>>>>>>>>>> Ectocarpus >>>>>>>> portal. I have created an accounted and started to work. Is it >>>>>>>> possible to download the set of predicted protein sequences? It >>>>>>>> would suit me better to do some local stand-alone searches >>>>>>>> (BLAST, >>>>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks >>>>>>>>>>>>> again, >>>>>>>>>>>>> Marek >>>>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>>>>>> login/password. You can use this login to access the ectocarpus >>>>>>>> wiki >>>>>>>>>>>>>> as >>>>>>>>>>>>>> well, >>>>>>>>>>>>>> Kenny >>>>>>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark >>>>>>>>>>>>>>> Cock >>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>>>>>> portal and redirected us to you for obtaining a password >>>>>>>>>>>>>>> to >>>>>>>>>>>>>>> the >>>>>>>> portal. I have one to the BLAST page at the Ghent web site >>>>>>>> (user: ectocarpus, password: sillysilly) but it does not work >>>>>>>> for the portal at >>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> this >>>>>>>> is not the right link to the portal, so please, let me know how >>>>>>>> can >>>>>>>> I >>>>>>>> access the portal so taht I can start annotating. Thank >>>>>>>> you in advance and best regards, >>>>>>>>>>>>>>> Marek Elias >>>>>>>>>>>>>>> Department of Botany >>>>>>>>>>>>>>> Faculty of Science >>>>>>>>>>>>>>> Charles University >>>>>>>>>>>>>>> Benatska 2 >>>>>>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>>>>>> Czech Republic >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> ================================================================== >>>>>>>> Kenny Billiau >>>>>>>>>>>>>> Web Developer >>>>>>>>>>>>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>>>>>>>>>>>> 3313809 >>>>>>>> VIB Department of Plant Systems Biology, Ghent University >>>>>>>>>>>>>> Technologiepark 927, 9052 Gent, BELGIUM >>>>>>>>>>>>>> kenny.billiau(a)psb.ugent.be >>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be >>>>>>>> ================================================================== >>>>>>>>>>>> -- >>>>>>>>>>>> ============================================================== >>>>>>>>>>>> Lieven >>>>>>>> Sterck Predoctoral fellow Tel:+32 >>>>>>>> (0)9 >>>>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department >>>>>>>> of >>>>>>>> Plant >>>>>>>> Systems Biology, UGent >>>>>>>>>>>> Bioinformatics and Evolutionary Genomics Division >>>>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium >>>>>>>>>>>> Email: >>>>>>>> lieven.sterck(a)psb.ugent.be >>>>>>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>>> Algal >>>>>>>> Genetics Group >>>>>>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>>>>>> VÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©gÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©taux >>>>>>>>>>>> Marins et >>>>>>>>>>>> BiomolÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©cules (Marine >>>>>>>>>>>> Plants and >>>>>>>>>>>> Biomolecules) >>>>>>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>>>>>> 29682 Roscoff Cedex, France >>>>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>>>>>> ============================================================== >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > >

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[Beg-bogas] [Fwd: Re: [Fwd: Re: Ectocarpus proteins]]
by Lieven Sterck 17 Nov '07

17 Nov '07

guys, i fixed this prob (temporarly), but the seq is still 'there' in the POST call. any way we can get around that?? thx, L. ---------------------------- Original Message ---------------------------- Subject: Re: [Fwd: Re: Ectocarpus proteins] From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> Date: Sat, November 17, 2007 12:18 am To: melias(a)natur.cuni.cz -------------------------------------------------------------------------- Hi Marek, We fixed the download problem. The problem was indeed that it was to large to be shown on the screen. Now you will be notified of this and the sequence will not be shown, but you can still do 'save as fasta'. I hope this suites you. grtz, lieven > Hi Lieven, > > I am not able to download the nucleotide sequence of the supercontig > sctg_0. After clicking on the hyperlink "F" in the BLAST output the > sequence cannot be downloaded and the browser replies with an error > message. However, other supercontig sequences can be displayed by > clicking on the corresponding hyperlink on the very same BLAST output > page. I do not understand at all what is going on. > Thanks, > Marek > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> Hi Marek, >> >> This is interesting information! >> I'm (our lab is) not responsible for producing the sequence, that job is >> done by GenoScope. >> >> The best you can do for the moment is report these kind of information >> on >> the wiki-page or in the structure comment field on the edit page >> (preferably in both :-) ). >> If the sequences is missing (Ns) than there is nothing much we can do >> (have you tried searching the Ectsi_Inf2kb blast database? maybe the >> missign piece is presen but not assembled into a larger contig??). >> If you notice that a gene has been 'split' over two contigs, we can >> report >> this to the sequencing center and they can use it for making a next >> assembly. >> >> grtz, >> lieven >> >> >>> Hi Lieven, >>> >>> I really highly appreciate your prompt assistance. I will probably >>> never cease having additionals troubles - here is another such: what >>> shoul I do if I found that it is impossible to create the correct gene >>> model because the underlying genome sequence is incomplete? Or even >>> worse, what to do with genes split into two separate supercontigs? For >>> example the models Esi0169_0001 and Esi0169_0002 on the very beginning >>> of the supercontig sctg_169 actually represent fragments of a signle >>> gene, whose intial exon is not repesented on the supercontig but seems >>> to reside near the 3' end of the small supercontig sctg_945. You >>> probably do not have any data linking these supercontigs together but >>> I have very good reasons to believe that they belong together, because >>> the gene is very vell conserved and the two pieces encoded by the two >>> supercontigs fit into the expected structure of the gene. How should I >>> annotate the gene? >>> Thanks, >>> Marek >>> >>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>> >>>> Hi Marek, >>>> >>>> This is a not so easy issue (for us! not for you). >>>> the best option would be to select the model labeled 'CDS' and then >>>> insert >>>> your new coordinates. The other models you can ignore. >>>> >>>> grtz, >>>> lieven >>>> >>>>> Hi Lieven, >>>>> >>>>> thanks for the comments, it now seems that he problem with saving the >>>>> changes of gene models has been solved. I am sorry, however, to say >>>>> that I have just encountered another point requiring a discussion >>>>> with >>>>> you. I found that some genes I am annotating are incorrectly >>>>> predicted >>>>> as two or even three independent loci. How to correct these >>>>> instances? >>>>> Should I merge somehow the models into one, which I subsequetly >>>>> modify >>>>> bu inserting correct coordinates? If yes, how should I do it? Or >>>>> should I simply insert the correct coordinates into a field of one of >>>>> the partial "submodels" and ignore or delete the remaining? >>>>> Thanks, >>>>> Marek >>>>> >>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>> >>>>>> Hi Marek, >>>>>> >>>>>> I spotted the problem. You are talking about locus Esi0425_0013, no? >>>>>> I can see that you made an edit in the DB, but the problem is that >>>>>> there >>>>>> seems to be a double save. If you check in the history the last-1 >>>>>> date >>>>>> you'll see your edit. >>>>>> >>>>>> We are sorting this out as quickly as possible. >>>>>> >>>>>> best regards, >>>>>> lieven >>>>>> >>>>>> >>>>>>> Dear Lieven, >>>>>>> >>>>>>> thanks for the change in artemini, this is exactly what I think >>>>>>> will >>>>>>> make the annotation much more straightforward. I checked the system >>>>>>> with one gene (correcting coordinates of one exon). I saved the >>>>>>> modified coordinates using "Save to server" command in "File" menu >>>>>>> option, but the model has not changed in the database yet. Are you >>>>>>> reviewing opur annotations before incorporating them into the >>>>>>> database? Or what is going on? >>>>>>> Thanks. Cheers, >>>>>>> >>>>>>> Marek >>>>>>> >>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> we made some adjustments to the artemini functionality and as a >>>>>>>> result >>>>>>>> the >>>>>>>> coordinates you see in the artemini window are now the same as in >>>>>>>> the >>>>>>>> webpage (= they are in reference to the whole scaffold). >>>>>>>> You can just copy and paste your coordinates into the artemini, >>>>>>>> save >>>>>>>> it >>>>>>>> and they will be entered into the DB. >>>>>>>> >>>>>>>> I hope this can satisfy your needs. If not, please do let me know, >>>>>>>> so >>>>>>>> we >>>>>>>> can think of better solution. >>>>>>>> >>>>>>>> thanks and best regards, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: Re: Ectocarpus proteins >>>>>>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>>>>>> Date: Thu, November 8, 2007 11:17 pm >>>>>>>> To: melias(a)natur.cuni.cz >>>>>>>> Cc: cock(a)sb-roscoff.fr >>>>>>>> beg-bogas(a)psb.ugent.be >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> You can find a manual on how to use the artemis tool on the Sanger >>>>>>>> Institute website. >>>>>>>> May I inquire if you find the artemis tool itself not >>>>>>>> user-friendly >>>>>>>> or >>>>>>>> rather the way it is incoporated in the portal? >>>>>>>> >>>>>>>> The coordinates in the artemini view differ indeed from the ones >>>>>>>> on >>>>>>>> the >>>>>>>> webpage. this is because the sequence you get to see in the >>>>>>>> artemini >>>>>>>> view >>>>>>>> is only a subpart of the whole scaffold (this in order to let the >>>>>>>> procedure go faster). The coordinates you see in artemini are in >>>>>>>> reference >>>>>>>> to the subpart while you have (and also on the webpage) them in >>>>>>>> reference >>>>>>>> of the whole scaffold. >>>>>>>> >>>>>>>> In theory it is possible to make the coordinates 'box' editable. >>>>>>>> but, >>>>>>>> ... >>>>>>>> i'm a little bit reluctant to do this due to bad experience with >>>>>>>> this >>>>>>>> approach in previous projects. We noticied it is very easy to >>>>>>>> include >>>>>>>> mistakes this way (aspecially for non experienced annotators). >>>>>>>> That >>>>>>>> is >>>>>>>> why >>>>>>>> we include the artemini system in this version (where some basic >>>>>>>> checks >>>>>>>> on >>>>>>>> the structure are performed and you have the visual check of the >>>>>>>> structure). >>>>>>>> But I also completely understand your point that for more >>>>>>>> experienced >>>>>>>> users this might not be ideal... >>>>>>>> What we also can do is to add a function in the artemini to >>>>>>>> 'transfer' >>>>>>>> the >>>>>>>> coordinates you enter (in reference of the whole scaffold) onto >>>>>>>> the >>>>>>>> subpart in artemini. That way you could just paste your >>>>>>>> coordinates >>>>>>>> into >>>>>>>> the coordinate box of artemini, push the 'transfer' button and >>>>>>>> they >>>>>>>> will >>>>>>>> be adjusted onto the subpart. You can then also profit from the >>>>>>>> visual >>>>>>>> check. When you then save your modifications they will be entered >>>>>>>> to >>>>>>>> the >>>>>>>> DB. >>>>>>>> Do you think this might be more useful? or does it still sounds to >>>>>>>> much >>>>>>>> of >>>>>>>> a hastle? >>>>>>>> >>>>>>>> best and thanks for the feedback, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>>> Dear Lieven, >>>>>>>>> >>>>>>>>> thanks for the link, I have successfully downloaded the protein >>>>>>>>> database. I would like to start making corrections of the gene >>>>>>>>> models >>>>>>>>> I >>>>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is >>>>>>>> there >>>>>>>> any >>>>>>>> manual how to work with the Artemini tool? I found it not be too >>>>>>>> user-friendly. For instance, I do not understand why the exon >>>>>>>> coordinates indicated by Artemini differs from the actual >>>>>>>> coordinates >>>>>>>> on >>>>>>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>>>>>> coordinates, with an incorrect first exon, are as follows: >>>>>>>>> >>>>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> I would like to change the first exon so that the coordinates are >>>>>>>>> like >>>>>>>> this: >>>>>>>>> >>>>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> The coordinates given for this gene in Artemini are as follows: >>>>>>>>> >>>>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>>>>>> >>>>>>>>> Why there is the difference? I have to say that I would highly >>>>>>>>> appreciate if it is possible to edit gene models just by typing >>>>>>>>> the >>>>>>>> correct coordinates of exons I found by comparing my CDS models >>>>>>>> with >>>>>>>> the >>>>>>>> contig sequence. Is this possible? >>>>>>>>> Thank you and best regards, >>>>>>>>> >>>>>>>>> Marek E. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>> >>>>>>>>>> Dear Marek, >>>>>>>>>> the download is available from this address: >>>>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>>>>>> (login/passw : psbguest/ectocarpus) >>>>>>>>>> Apologises that I haven't informed you earlier, it is quite >>>>>>>>>> hectic >>>>>>>>>> for >>>>>>>> the >>>>>>>>>> moment. >>>>>>>>>> please let me know if this doesn't work. >>>>>>>>>> best regards, >>>>>>>>>> lieven >>>>>>>>>>> Dear Lieven, >>>>>>>>>>> you mentioned that from this week's Monday the whole predicted >>>>>>>> proteome of Ectocarpus should be available for download. I tried >>>>>>>> to >>>>>>>> find >>>>>>>> a >>>>>>>> link to the file at BOGAS web page but haven't found any. Could >>>>>>>> you, >>>>>>>> please, let me know, where to go for the downloading? >>>>>>>>>>> Thanks, best regards, >>>>>>>>>>> Marek Elias >>>>>>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>>>> Dear Marek, >>>>>>>>>>>> From monday on you will be able to download all predicted >>>>>>>>>>>> protein/genes >>>>>>>>>>>> in batch. >>>>>>>>>>>> sorry for the delay. >>>>>>>>>>>> regards, >>>>>>>>>>>> lieven >>>>>>>>>>>> Kenny Billiau wrote: >>>>>>>>>>>>> -------- Original Message -------- >>>>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>>>>>> References: >>>>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>>>>>> Hi Kenny, >>>>>>>>>>>>> thanks for the advice with getting the access to the >>>>>>>>>>>>> Ectocarpus >>>>>>>> portal. I have created an accounted and started to work. Is it >>>>>>>> possible to download the set of predicted protein sequences? It >>>>>>>> would suit me better to do some local stand-alone searches >>>>>>>> (BLAST, >>>>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks >>>>>>>>>>>>> again, >>>>>>>>>>>>> Marek >>>>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>>>>>> login/password. You can use this login to access the ectocarpus >>>>>>>> wiki >>>>>>>>>>>>>> as >>>>>>>>>>>>>> well, >>>>>>>>>>>>>> Kenny >>>>>>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark >>>>>>>>>>>>>>> Cock >>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>>>>>> portal and redirected us to you for obtaining a password >>>>>>>>>>>>>>> to >>>>>>>>>>>>>>> the >>>>>>>> portal. I have one to the BLAST page at the Ghent web site >>>>>>>> (user: ectocarpus, password: sillysilly) but it does not work >>>>>>>> for the portal at >>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> this >>>>>>>> is not the right link to the portal, so please, let me know how >>>>>>>> can >>>>>>>> I >>>>>>>> access the portal so taht I can start annotating. Thank >>>>>>>> you in advance and best regards, >>>>>>>>>>>>>>> Marek Elias >>>>>>>>>>>>>>> Department of Botany >>>>>>>>>>>>>>> Faculty of Science >>>>>>>>>>>>>>> Charles University >>>>>>>>>>>>>>> Benatska 2 >>>>>>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>>>>>> Czech Republic >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> ================================================================== >>>>>>>> Kenny Billiau >>>>>>>>>>>>>> Web Developer >>>>>>>>>>>>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>>>>>>>>>>>> 3313809 >>>>>>>> VIB Department of Plant Systems Biology, Ghent University >>>>>>>>>>>>>> Technologiepark 927, 9052 Gent, BELGIUM >>>>>>>>>>>>>> kenny.billiau(a)psb.ugent.be >>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be >>>>>>>> ================================================================== >>>>>>>>>>>> -- >>>>>>>>>>>> ============================================================== >>>>>>>>>>>> Lieven >>>>>>>> Sterck Predoctoral fellow Tel:+32 >>>>>>>> (0)9 >>>>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department >>>>>>>> of >>>>>>>> Plant >>>>>>>> Systems Biology, UGent >>>>>>>>>>>> Bioinformatics and Evolutionary Genomics Division >>>>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium >>>>>>>>>>>> Email: >>>>>>>> lieven.sterck(a)psb.ugent.be >>>>>>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>>> Algal >>>>>>>> Genetics Group >>>>>>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>>>>>> VÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©gÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©taux >>>>>>>>>>>> Marins et >>>>>>>>>>>> BiomolÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©cules (Marine >>>>>>>>>>>> Plants and >>>>>>>>>>>> Biomolecules) >>>>>>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>>>>>> 29682 Roscoff Cedex, France >>>>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>>>>>> ============================================================== >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > >

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[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by Lieven Sterck 17 Nov '07

17 Nov '07

Hi Marek, I tried it myself and I think it's due to the size of the scaffold. It is to big to be displayed on a page (it also happens with other large scaffolds apparently). We see how we can work around it. sorry and thanks for noticing this, best regards, lieven > Hi Lieven, > > I am not able to download the nucleotide sequence of the supercontig > sctg_0. After clicking on the hyperlink "F" in the BLAST output the > sequence cannot be downloaded and the browser replies with an error > message. However, other supercontig sequences can be displayed by > clicking on the corresponding hyperlink on the very same BLAST output > page. I do not understand at all what is going on. > Thanks, > Marek > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> Hi Marek, >> >> This is interesting information! >> I'm (our lab is) not responsible for producing the sequence, that job is >> done by GenoScope. >> >> The best you can do for the moment is report these kind of information >> on >> the wiki-page or in the structure comment field on the edit page >> (preferably in both :-) ). >> If the sequences is missing (Ns) than there is nothing much we can do >> (have you tried searching the Ectsi_Inf2kb blast database? maybe the >> missign piece is presen but not assembled into a larger contig??). >> If you notice that a gene has been 'split' over two contigs, we can >> report >> this to the sequencing center and they can use it for making a next >> assembly. >> >> grtz, >> lieven >> >> >>> Hi Lieven, >>> >>> I really highly appreciate your prompt assistance. I will probably >>> never cease having additionals troubles - here is another such: what >>> shoul I do if I found that it is impossible to create the correct gene >>> model because the underlying genome sequence is incomplete? Or even >>> worse, what to do with genes split into two separate supercontigs? For >>> example the models Esi0169_0001 and Esi0169_0002 on the very beginning >>> of the supercontig sctg_169 actually represent fragments of a signle >>> gene, whose intial exon is not repesented on the supercontig but seems >>> to reside near the 3' end of the small supercontig sctg_945. You >>> probably do not have any data linking these supercontigs together but >>> I have very good reasons to believe that they belong together, because >>> the gene is very vell conserved and the two pieces encoded by the two >>> supercontigs fit into the expected structure of the gene. How should I >>> annotate the gene? >>> Thanks, >>> Marek >>> >>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>> >>>> Hi Marek, >>>> >>>> This is a not so easy issue (for us! not for you). >>>> the best option would be to select the model labeled 'CDS' and then >>>> insert >>>> your new coordinates. The other models you can ignore. >>>> >>>> grtz, >>>> lieven >>>> >>>>> Hi Lieven, >>>>> >>>>> thanks for the comments, it now seems that he problem with saving the >>>>> changes of gene models has been solved. I am sorry, however, to say >>>>> that I have just encountered another point requiring a discussion >>>>> with >>>>> you. I found that some genes I am annotating are incorrectly >>>>> predicted >>>>> as two or even three independent loci. How to correct these >>>>> instances? >>>>> Should I merge somehow the models into one, which I subsequetly >>>>> modify >>>>> bu inserting correct coordinates? If yes, how should I do it? Or >>>>> should I simply insert the correct coordinates into a field of one of >>>>> the partial "submodels" and ignore or delete the remaining? >>>>> Thanks, >>>>> Marek >>>>> >>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>> >>>>>> Hi Marek, >>>>>> >>>>>> I spotted the problem. You are talking about locus Esi0425_0013, no? >>>>>> I can see that you made an edit in the DB, but the problem is that >>>>>> there >>>>>> seems to be a double save. If you check in the history the last-1 >>>>>> date >>>>>> you'll see your edit. >>>>>> >>>>>> We are sorting this out as quickly as possible. >>>>>> >>>>>> best regards, >>>>>> lieven >>>>>> >>>>>> >>>>>>> Dear Lieven, >>>>>>> >>>>>>> thanks for the change in artemini, this is exactly what I think >>>>>>> will >>>>>>> make the annotation much more straightforward. I checked the system >>>>>>> with one gene (correcting coordinates of one exon). I saved the >>>>>>> modified coordinates using "Save to server" command in "File" menu >>>>>>> option, but the model has not changed in the database yet. Are you >>>>>>> reviewing opur annotations before incorporating them into the >>>>>>> database? Or what is going on? >>>>>>> Thanks. Cheers, >>>>>>> >>>>>>> Marek >>>>>>> >>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> we made some adjustments to the artemini functionality and as a >>>>>>>> result >>>>>>>> the >>>>>>>> coordinates you see in the artemini window are now the same as in >>>>>>>> the >>>>>>>> webpage (= they are in reference to the whole scaffold). >>>>>>>> You can just copy and paste your coordinates into the artemini, >>>>>>>> save >>>>>>>> it >>>>>>>> and they will be entered into the DB. >>>>>>>> >>>>>>>> I hope this can satisfy your needs. If not, please do let me know, >>>>>>>> so >>>>>>>> we >>>>>>>> can think of better solution. >>>>>>>> >>>>>>>> thanks and best regards, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: Re: Ectocarpus proteins >>>>>>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>>>>>> Date: Thu, November 8, 2007 11:17 pm >>>>>>>> To: melias(a)natur.cuni.cz >>>>>>>> Cc: cock(a)sb-roscoff.fr >>>>>>>> beg-bogas(a)psb.ugent.be >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> You can find a manual on how to use the artemis tool on the Sanger >>>>>>>> Institute website. >>>>>>>> May I inquire if you find the artemis tool itself not >>>>>>>> user-friendly >>>>>>>> or >>>>>>>> rather the way it is incoporated in the portal? >>>>>>>> >>>>>>>> The coordinates in the artemini view differ indeed from the ones >>>>>>>> on >>>>>>>> the >>>>>>>> webpage. this is because the sequence you get to see in the >>>>>>>> artemini >>>>>>>> view >>>>>>>> is only a subpart of the whole scaffold (this in order to let the >>>>>>>> procedure go faster). The coordinates you see in artemini are in >>>>>>>> reference >>>>>>>> to the subpart while you have (and also on the webpage) them in >>>>>>>> reference >>>>>>>> of the whole scaffold. >>>>>>>> >>>>>>>> In theory it is possible to make the coordinates 'box' editable. >>>>>>>> but, >>>>>>>> ... >>>>>>>> i'm a little bit reluctant to do this due to bad experience with >>>>>>>> this >>>>>>>> approach in previous projects. We noticied it is very easy to >>>>>>>> include >>>>>>>> mistakes this way (aspecially for non experienced annotators). >>>>>>>> That >>>>>>>> is >>>>>>>> why >>>>>>>> we include the artemini system in this version (where some basic >>>>>>>> checks >>>>>>>> on >>>>>>>> the structure are performed and you have the visual check of the >>>>>>>> structure). >>>>>>>> But I also completely understand your point that for more >>>>>>>> experienced >>>>>>>> users this might not be ideal... >>>>>>>> What we also can do is to add a function in the artemini to >>>>>>>> 'transfer' >>>>>>>> the >>>>>>>> coordinates you enter (in reference of the whole scaffold) onto >>>>>>>> the >>>>>>>> subpart in artemini. That way you could just paste your >>>>>>>> coordinates >>>>>>>> into >>>>>>>> the coordinate box of artemini, push the 'transfer' button and >>>>>>>> they >>>>>>>> will >>>>>>>> be adjusted onto the subpart. You can then also profit from the >>>>>>>> visual >>>>>>>> check. When you then save your modifications they will be entered >>>>>>>> to >>>>>>>> the >>>>>>>> DB. >>>>>>>> Do you think this might be more useful? or does it still sounds to >>>>>>>> much >>>>>>>> of >>>>>>>> a hastle? >>>>>>>> >>>>>>>> best and thanks for the feedback, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>>> Dear Lieven, >>>>>>>>> >>>>>>>>> thanks for the link, I have successfully downloaded the protein >>>>>>>>> database. I would like to start making corrections of the gene >>>>>>>>> models >>>>>>>>> I >>>>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is >>>>>>>> there >>>>>>>> any >>>>>>>> manual how to work with the Artemini tool? I found it not be too >>>>>>>> user-friendly. For instance, I do not understand why the exon >>>>>>>> coordinates indicated by Artemini differs from the actual >>>>>>>> coordinates >>>>>>>> on >>>>>>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>>>>>> coordinates, with an incorrect first exon, are as follows: >>>>>>>>> >>>>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> I would like to change the first exon so that the coordinates are >>>>>>>>> like >>>>>>>> this: >>>>>>>>> >>>>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> The coordinates given for this gene in Artemini are as follows: >>>>>>>>> >>>>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>>>>>> >>>>>>>>> Why there is the difference? I have to say that I would highly >>>>>>>>> appreciate if it is possible to edit gene models just by typing >>>>>>>>> the >>>>>>>> correct coordinates of exons I found by comparing my CDS models >>>>>>>> with >>>>>>>> the >>>>>>>> contig sequence. Is this possible? >>>>>>>>> Thank you and best regards, >>>>>>>>> >>>>>>>>> Marek E. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>> >>>>>>>>>> Dear Marek, >>>>>>>>>> the download is available from this address: >>>>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>>>>>> (login/passw : psbguest/ectocarpus) >>>>>>>>>> Apologises that I haven't informed you earlier, it is quite >>>>>>>>>> hectic >>>>>>>>>> for >>>>>>>> the >>>>>>>>>> moment. >>>>>>>>>> please let me know if this doesn't work. >>>>>>>>>> best regards, >>>>>>>>>> lieven >>>>>>>>>>> Dear Lieven, >>>>>>>>>>> you mentioned that from this week's Monday the whole predicted >>>>>>>> proteome of Ectocarpus should be available for download. I tried >>>>>>>> to >>>>>>>> find >>>>>>>> a >>>>>>>> link to the file at BOGAS web page but haven't found any. Could >>>>>>>> you, >>>>>>>> please, let me know, where to go for the downloading? >>>>>>>>>>> Thanks, best regards, >>>>>>>>>>> Marek Elias >>>>>>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>>>> Dear Marek, >>>>>>>>>>>> From monday on you will be able to download all predicted >>>>>>>>>>>> protein/genes >>>>>>>>>>>> in batch. >>>>>>>>>>>> sorry for the delay. >>>>>>>>>>>> regards, >>>>>>>>>>>> lieven >>>>>>>>>>>> Kenny Billiau wrote: >>>>>>>>>>>>> -------- Original Message -------- >>>>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>>>>>> References: >>>>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>>>>>> Hi Kenny, >>>>>>>>>>>>> thanks for the advice with getting the access to the >>>>>>>>>>>>> Ectocarpus >>>>>>>> portal. I have created an accounted and started to work. Is it >>>>>>>> possible to download the set of predicted protein sequences? It >>>>>>>> would suit me better to do some local stand-alone searches >>>>>>>> (BLAST, >>>>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks >>>>>>>>>>>>> again, >>>>>>>>>>>>> Marek >>>>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>>>>>> login/password. You can use this login to access the ectocarpus >>>>>>>> wiki >>>>>>>>>>>>>> as >>>>>>>>>>>>>> well, >>>>>>>>>>>>>> Kenny >>>>>>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark >>>>>>>>>>>>>>> Cock >>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>>>>>> portal and redirected us to you for obtaining a password >>>>>>>>>>>>>>> to >>>>>>>>>>>>>>> the >>>>>>>> portal. I have one to the BLAST page at the Ghent web site >>>>>>>> (user: ectocarpus, password: sillysilly) but it does not work >>>>>>>> for the portal at >>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> this >>>>>>>> is not the right link to the portal, so please, let me know how >>>>>>>> can >>>>>>>> I >>>>>>>> access the portal so taht I can start annotating. Thank >>>>>>>> you in advance and best regards, >>>>>>>>>>>>>>> Marek Elias >>>>>>>>>>>>>>> Department of Botany >>>>>>>>>>>>>>> Faculty of Science >>>>>>>>>>>>>>> Charles University >>>>>>>>>>>>>>> Benatska 2 >>>>>>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>>>>>> Czech Republic >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> ================================================================== >>>>>>>> Kenny Billiau >>>>>>>>>>>>>> Web Developer >>>>>>>>>>>>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>>>>>>>>>>>> 3313809 >>>>>>>> VIB Department of Plant Systems Biology, Ghent University >>>>>>>>>>>>>> Technologiepark 927, 9052 Gent, BELGIUM >>>>>>>>>>>>>> kenny.billiau(a)psb.ugent.be >>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be >>>>>>>> ================================================================== >>>>>>>>>>>> -- >>>>>>>>>>>> ============================================================== >>>>>>>>>>>> Lieven >>>>>>>> Sterck Predoctoral fellow Tel:+32 >>>>>>>> (0)9 >>>>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department >>>>>>>> of >>>>>>>> Plant >>>>>>>> Systems Biology, UGent >>>>>>>>>>>> Bioinformatics and Evolutionary Genomics Division >>>>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium >>>>>>>>>>>> Email: >>>>>>>> lieven.sterck(a)psb.ugent.be >>>>>>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>>> Algal >>>>>>>> Genetics Group >>>>>>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>>>>>> VÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©gÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©taux >>>>>>>>>>>> Marins et >>>>>>>>>>>> BiomolÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©cules (Marine >>>>>>>>>>>> Plants and >>>>>>>>>>>> Biomolecules) >>>>>>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>>>>>> 29682 Roscoff Cedex, France >>>>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>>>>>> ============================================================== >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > >

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Re: [Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by Thomas Abeel 16 Nov '07

16 Nov '07

De oorzaak is dat de nieuwe coordinate die hij opgeeft buiten de sequentie in de gepadde Ns vallen. Waardoor dat in eerste instantie lijkt te lukken, maar dan gaat Artemini de mist in bij het saven omdat hij probeert die coordinaten aan te passen, wat niet gaat omdat die negatief worden. De enige mogelijkheid die ik hier zie is om meer sequentie door te geven zodat Artemini niet zoveel moet padden. Ofwel EMBL formaat uitbreiden zodat die ook negatieve coordinaten aankan. Maar hoe dan ook lijkt me dat nogal veel werk. Mij lijkt het eerste (meer/alle sequentie) het eenvoudigste. T Lieven Sterck schreef: > no problemo!! > gheb tan ook conge, wa ;-) > > tkan trouwens ook in de perl zitten ... > > L. > > >> Dat zal voor morgen zijn zenne. >> >> T >> >> >> Lieven Sterck schreef: >> >>> Hi Marek, >>> >>> sorry for that! >>> We'll look into it. >>> >>> thanks, >>> lieven >>> >>> >>> >>> >>>> Hi Lieven, >>>> >>>> I am working hard on the annotation but unfortunatelly still some >>>> unexpected problems emerge. Now I face a trouble with annotating the >>>> gene Esi0030_0124. When I insert the correct coordinates, which are as >>>> follows: >>>> >>>> 570185..570280,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 >>>> >>>> However, after I try to save the change to the server, the program >>>> replies with an error message, and when I open the window with the >>>> coordinates, they are changed so that they look like this: >>>> >>>> 2,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 >>>> >>>> I have not seen this behaviour with other genes, so I have no >>>> explanation for it. What is going on? >>>> >>>> Thanks, >>>> Marek >>>> >>>> >>>> >>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>> >>>> >>>> >>>>> Hi Marek, >>>>> >>>>> This is a not so easy issue (for us! not for you). >>>>> the best option would be to select the model labeled 'CDS' and then >>>>> insert >>>>> your new coordinates. The other models you can ignore. >>>>> >>>>> grtz, >>>>> lieven >>>>> >>>>> >>>>> >>>>>> Hi Lieven, >>>>>> >>>>>> thanks for the comments, it now seems that he problem with saving the >>>>>> changes of gene models has been solved. I am sorry, however, to say >>>>>> that I have just encountered another point requiring a discussion >>>>>> with >>>>>> you. I found that some genes I am annotating are incorrectly >>>>>> predicted >>>>>> as two or even three independent loci. How to correct these >>>>>> instances? >>>>>> Should I merge somehow the models into one, which I subsequetly >>>>>> modify >>>>>> bu inserting correct coordinates? If yes, how should I do it? Or >>>>>> should I simply insert the correct coordinates into a field of one of >>>>>> the partial "submodels" and ignore or delete the remaining? >>>>>> Thanks, >>>>>> Marek >>>>>> >>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>> >>>>>> >>>>>> >>>>>>> Hi Marek, >>>>>>> >>>>>>> I spotted the problem. You are talking about locus Esi0425_0013, no? >>>>>>> I can see that you made an edit in the DB, but the problem is that >>>>>>> there >>>>>>> seems to be a double save. If you check in the history the last-1 >>>>>>> date >>>>>>> you'll see your edit. >>>>>>> >>>>>>> We are sorting this out as quickly as possible. >>>>>>> >>>>>>> best regards, >>>>>>> lieven >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Dear Lieven, >>>>>>>> >>>>>>>> thanks for the change in artemini, this is exactly what I think >>>>>>>> will >>>>>>>> make the annotation much more straightforward. I checked the system >>>>>>>> with one gene (correcting coordinates of one exon). I saved the >>>>>>>> modified coordinates using "Save to server" command in "File" menu >>>>>>>> option, but the model has not changed in the database yet. Are you >>>>>>>> reviewing opur annotations before incorporating them into the >>>>>>>> database? Or what is going on? >>>>>>>> Thanks. Cheers, >>>>>>>> >>>>>>>> Marek >>>>>>>> >>>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Dear Marek, >>>>>>>>> >>>>>>>>> we made some adjustments to the artemini functionality and as a >>>>>>>>> result >>>>>>>>> the >>>>>>>>> coordinates you see in the artemini window are now the same as in >>>>>>>>> the >>>>>>>>> webpage (= they are in reference to the whole scaffold). >>>>>>>>> You can just copy and paste your coordinates into the artemini, >>>>>>>>> save >>>>>>>>> it >>>>>>>>> and they will be entered into the DB. >>>>>>>>> >>>>>>>>> I hope this can satisfy your needs. If not, please do let me know, >>>>>>>>> so >>>>>>>>> we >>>>>>>>> can think of better solution. >>>>>>>>> >>>>>>>>> thanks and best regards, >>>>>>>>> lieven >>>>>>>>> >>>>>>>>> >>>>>>>>> ---------------------------- Original Message >>>>>>>>> ---------------------------- >>>>>>>>> Subject: Re: Ectocarpus proteins >>>>>>>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>>>>>>> Date: Thu, November 8, 2007 11:17 pm >>>>>>>>> To: melias(a)natur.cuni.cz >>>>>>>>> Cc: cock(a)sb-roscoff.fr >>>>>>>>> beg-bogas(a)psb.ugent.be >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> >>>>>>>>> Dear Marek, >>>>>>>>> >>>>>>>>> You can find a manual on how to use the artemis tool on the Sanger >>>>>>>>> Institute website. >>>>>>>>> May I inquire if you find the artemis tool itself not >>>>>>>>> user-friendly >>>>>>>>> or >>>>>>>>> rather the way it is incoporated in the portal? >>>>>>>>> >>>>>>>>> The coordinates in the artemini view differ indeed from the ones >>>>>>>>> on >>>>>>>>> the >>>>>>>>> webpage. this is because the sequence you get to see in the >>>>>>>>> artemini >>>>>>>>> view >>>>>>>>> is only a subpart of the whole scaffold (this in order to let the >>>>>>>>> procedure go faster). The coordinates you see in artemini are in >>>>>>>>> reference >>>>>>>>> to the subpart while you have (and also on the webpage) them in >>>>>>>>> reference >>>>>>>>> of the whole scaffold. >>>>>>>>> >>>>>>>>> In theory it is possible to make the coordinates 'box' editable. >>>>>>>>> but, >>>>>>>>> ... >>>>>>>>> i'm a little bit reluctant to do this due to bad experience with >>>>>>>>> this >>>>>>>>> approach in previous projects. We noticied it is very easy to >>>>>>>>> include >>>>>>>>> mistakes this way (aspecially for non experienced annotators). >>>>>>>>> That >>>>>>>>> is >>>>>>>>> why >>>>>>>>> we include the artemini system in this version (where some basic >>>>>>>>> checks >>>>>>>>> on >>>>>>>>> the structure are performed and you have the visual check of the >>>>>>>>> structure). >>>>>>>>> But I also completely understand your point that for more >>>>>>>>> experienced >>>>>>>>> users this might not be ideal... >>>>>>>>> What we also can do is to add a function in the artemini to >>>>>>>>> 'transfer' >>>>>>>>> the >>>>>>>>> coordinates you enter (in reference of the whole scaffold) onto >>>>>>>>> the >>>>>>>>> subpart in artemini. That way you could just paste your >>>>>>>>> coordinates >>>>>>>>> into >>>>>>>>> the coordinate box of artemini, push the 'transfer' button and >>>>>>>>> they >>>>>>>>> will >>>>>>>>> be adjusted onto the subpart. You can then also profit from the >>>>>>>>> visual >>>>>>>>> check. When you then save your modifications they will be entered >>>>>>>>> to >>>>>>>>> the >>>>>>>>> DB. >>>>>>>>> Do you think this might be more useful? or does it still sounds to >>>>>>>>> much >>>>>>>>> of >>>>>>>>> a hastle? >>>>>>>>> >>>>>>>>> best and thanks for the feedback, >>>>>>>>> lieven >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Dear Lieven, >>>>>>>>>> >>>>>>>>>> thanks for the link, I have successfully downloaded the protein >>>>>>>>>> database. I would like to start making corrections of the gene >>>>>>>>>> models >>>>>>>>>> I >>>>>>>>>> >>>>>>>>>> >>>>>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is >>>>>>>>> there >>>>>>>>> any >>>>>>>>> manual how to work with the Artemini tool? I found it not be too >>>>>>>>> user-friendly. For instance, I do not understand why the exon >>>>>>>>> coordinates indicated by Artemini differs from the actual >>>>>>>>> coordinates >>>>>>>>> on >>>>>>>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>>>>>> >>>>>>>>> >>>>>>>>>> coordinates, with an incorrect first exon, are as follows: >>>>>>>>>> >>>>>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>>> >>>>>>>>>> I would like to change the first exon so that the coordinates are >>>>>>>>>> like >>>>>>>>>> >>>>>>>>>> >>>>>>>>> this: >>>>>>>>> >>>>>>>>> >>>>>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>>> >>>>>>>>>> The coordinates given for this gene in Artemini are as follows: >>>>>>>>>> >>>>>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>>>>>>> >>>>>>>>>> Why there is the difference? I have to say that I would highly >>>>>>>>>> appreciate if it is possible to edit gene models just by typing >>>>>>>>>> the >>>>>>>>>> >>>>>>>>>> >>>>>>>>> correct coordinates of exons I found by comparing my CDS models >>>>>>>>> with >>>>>>>>> the >>>>>>>>> contig sequence. Is this possible? >>>>>>>>> >>>>>>>>> >>>>>>>>>> Thank you and best regards, >>>>>>>>>> >>>>>>>>>> Marek E. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Dear Marek, >>>>>>>>>>> the download is available from this address: >>>>>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>>>>>>> (login/passw : psbguest/ectocarpus) >>>>>>>>>>> Apologises that I haven't informed you earlier, it is quite >>>>>>>>>>> hectic >>>>>>>>>>> for >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> the >>>>>>>>> >>>>>>>>> >>>>>>>>>>> moment. >>>>>>>>>>> please let me know if this doesn't work. >>>>>>>>>>> best regards, >>>>>>>>>>> lieven >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Dear Lieven, >>>>>>>>>>>> you mentioned that from this week's Monday the whole predicted >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>> proteome of Ectocarpus should be available for download. I tried >>>>>>>>> to >>>>>>>>> find >>>>>>>>> a >>>>>>>>> link to the file at BOGAS web page but haven't found any. Could >>>>>>>>> you, >>>>>>>>> please, let me know, where to go for the downloading? >>>>>>>>> >>>>>>>>> >>>>>>>>>>>> Thanks, best regards, >>>>>>>>>>>> Marek Elias >>>>>>>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> Dear Marek, >>>>>>>>>>>>> From monday on you will be able to download all predicted >>>>>>>>>>>>> protein/genes >>>>>>>>>>>>> in batch. >>>>>>>>>>>>> sorry for the delay. >>>>>>>>>>>>> regards, >>>>>>>>>>>>> lieven >>>>>>>>>>>>> Kenny Billiau wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> -------- Original Message -------- >>>>>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>>>>>>> References: >>>>>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>>>>>>> Hi Kenny, >>>>>>>>>>>>>> thanks for the advice with getting the access to the >>>>>>>>>>>>>> Ectocarpus >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>> portal. I have created an accounted and started to work. Is it >>>>>>>>> possible to download the set of predicted protein sequences? It >>>>>>>>> would suit me better to do some local stand-alone searches >>>>>>>>> (BLAST, >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks >>>>>>>>>>>>>> again, >>>>>>>>>>>>>> Marek >>>>>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>> login/password. You can use this login to access the ectocarpus >>>>>>>>> wiki >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> as >>>>>>>>>>>>>>> well, >>>>>>>>>>>>>>> Kenny >>>>>>>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark >>>>>>>>>>>>>>>> Cock >>>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>>>>>>> portal and redirected us to you for obtaining a password >>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>> portal. I have one to the BLAST page at the Ghent web site >>>>>>>>> (user: ectocarpus, password: sillysilly) but it does not work >>>>>>>>> for the portal at >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May >>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>> is not the right link to the portal, so please, let me know how >>>>>>>>> can >>>>>>>>> I >>>>>>>>> access the portal so taht I can start annotating. Thank >>>>>>>>> you in advance and best regards, >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>>> Marek Elias >>>>>>>>>>>>>>>> Department of Botany >>>>>>>>>>>>>>>> Faculty of Science >>>>>>>>>>>>>>>> Charles University >>>>>>>>>>>>>>>> Benatska 2 >>>>>>>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>>>>>>> Czech Republic >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> ================================================================== >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>> Kenny Billiau >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> Web Developer >>>>>>>>>>>>>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>>>>>>>>>>>>> 3313809 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>> VIB Department of Plant Systems Biology, Ghent University >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> Technologiepark 927, 9052 Gent, BELGIUM >>>>>>>>>>>>>>> kenny.billiau(a)psb.ugent.be >>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>> ================================================================== >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> ============================================================== >>>>>>>>>>>>> Lieven >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>> Sterck Predoctoral fellow Tel:+32 >>>>>>>>> (0)9 >>>>>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department >>>>>>>>> of >>>>>>>>> Plant >>>>>>>>> Systems Biology, UGent >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>> Bioinformatics and Evolutionary Genomics Division >>>>>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium >>>>>>>>>>>>> Email: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>> lieven.sterck(a)psb.ugent.be >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>>>> Algal >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>> Genetics Group >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>>>>>>> VÃƒÂƒÃ‚ÂƒÃƒÂ‚Ã‚Â©gÃƒÂƒÃ‚ÂƒÃƒÂ‚Ã‚Â©taux Marins et >>>>>>>>>>>>> BiomolÃƒÂƒÃ‚ÂƒÃƒÂ‚Ã‚Â©cules (Marine >>>>>>>>>>>>> Plants and >>>>>>>>>>>>> Biomolecules) >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>>> >>>>>>>>> >>>>>>>>>>>>> 29682 Roscoff Cedex, France >>>>>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>>>>>>> ============================================================== >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>> _______________________________________________ >>> Beg-bogas mailing list >>> Beg-bogas(a)psb.ugent.be >>> https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas >>> >>> > > >

2 1

[Beg-bogas] error_logs
by Kenny Billiau 16 Nov '07

16 Nov '07

hoi, Donderdag verplaatste IT enkele firewall rules zodanig dat alle data die naar onze webserver gaat door een monitor versie van mod_security gaat. En hoewel er wat problemen bleken met BOGAS, ligt het niet aan deze nieuwe opstelling. Monitor mode houdt geen requests tegen maar rapporteert deze enkel :) Er zijn GEEN foutmeldingen in de error logs. Enkele warnings op get_fast.pl, maar die requests komen er weldegelijk door. -Kenny -- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

1 0

[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by Lieven Sterck 16 Nov '07

16 Nov '07

Hi Marek, don't feel sorry. I'm on it. regards, lieven > Hi Lieven,, > I am deeply sorry, but two more problems emerged: > > 1. The Artemini tool fails to open for the following two models: > Esi0065_0017 and Esi0080_0048. After clicking on the "Modify using > Artemini" the Artemini starts to load but it stops with an error > message "The application encountered an unforseen error" > > 2. I tried several times to save the description of the Esi0000_0141 > gene, but the text filled into the "Short name" and "Definition" > fields always failed to be saved and the edit was not recorded in the > list of my 5 most recent annotations at the home page. > > Could you, pease, look also on these troubles? > Thanks, > Marek > > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> Hi Marek, >> >> sorry for that! >> We'll look into it. >> >> thanks, >> lieven >> >> >>> Hi Lieven, >>> >>> I am working hard on the annotation but unfortunatelly still some >>> unexpected problems emerge. Now I face a trouble with annotating the >>> gene Esi0030_0124. When I insert the correct coordinates, which are as >>> follows: >>> >>> 570185..570280,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 >>> >>> However, after I try to save the change to the server, the program >>> replies with an error message, and when I open the window with the >>> coordinates, they are changed so that they look like this: >>> >>> 2,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 >>> >>> I have not seen this behaviour with other genes, so I have no >>> explanation for it. What is going on? >>> >>> Thanks, >>> Marek >>> >>> >>> >>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>> >>>> Hi Marek, >>>> >>>> This is a not so easy issue (for us! not for you). >>>> the best option would be to select the model labeled 'CDS' and then >>>> insert >>>> your new coordinates. The other models you can ignore. >>>> >>>> grtz, >>>> lieven >>>> >>>>> Hi Lieven, >>>>> >>>>> thanks for the comments, it now seems that he problem with saving the >>>>> changes of gene models has been solved. I am sorry, however, to say >>>>> that I have just encountered another point requiring a discussion >>>>> with >>>>> you. I found that some genes I am annotating are incorrectly >>>>> predicted >>>>> as two or even three independent loci. How to correct these >>>>> instances? >>>>> Should I merge somehow the models into one, which I subsequetly >>>>> modify >>>>> bu inserting correct coordinates? If yes, how should I do it? Or >>>>> should I simply insert the correct coordinates into a field of one of >>>>> the partial "submodels" and ignore or delete the remaining? >>>>> Thanks, >>>>> Marek >>>>> >>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>> >>>>>> Hi Marek, >>>>>> >>>>>> I spotted the problem. You are talking about locus Esi0425_0013, no? >>>>>> I can see that you made an edit in the DB, but the problem is that >>>>>> there >>>>>> seems to be a double save. If you check in the history the last-1 >>>>>> date >>>>>> you'll see your edit. >>>>>> >>>>>> We are sorting this out as quickly as possible. >>>>>> >>>>>> best regards, >>>>>> lieven >>>>>> >>>>>> >>>>>>> Dear Lieven, >>>>>>> >>>>>>> thanks for the change in artemini, this is exactly what I think >>>>>>> will >>>>>>> make the annotation much more straightforward. I checked the system >>>>>>> with one gene (correcting coordinates of one exon). I saved the >>>>>>> modified coordinates using "Save to server" command in "File" menu >>>>>>> option, but the model has not changed in the database yet. Are you >>>>>>> reviewing opur annotations before incorporating them into the >>>>>>> database? Or what is going on? >>>>>>> Thanks. Cheers, >>>>>>> >>>>>>> Marek >>>>>>> >>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> we made some adjustments to the artemini functionality and as a >>>>>>>> result >>>>>>>> the >>>>>>>> coordinates you see in the artemini window are now the same as in >>>>>>>> the >>>>>>>> webpage (= they are in reference to the whole scaffold). >>>>>>>> You can just copy and paste your coordinates into the artemini, >>>>>>>> save >>>>>>>> it >>>>>>>> and they will be entered into the DB. >>>>>>>> >>>>>>>> I hope this can satisfy your needs. If not, please do let me know, >>>>>>>> so >>>>>>>> we >>>>>>>> can think of better solution. >>>>>>>> >>>>>>>> thanks and best regards, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: Re: Ectocarpus proteins >>>>>>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>>>>>> Date: Thu, November 8, 2007 11:17 pm >>>>>>>> To: melias(a)natur.cuni.cz >>>>>>>> Cc: cock(a)sb-roscoff.fr >>>>>>>> beg-bogas(a)psb.ugent.be >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Dear Marek, >>>>>>>> >>>>>>>> You can find a manual on how to use the artemis tool on the Sanger >>>>>>>> Institute website. >>>>>>>> May I inquire if you find the artemis tool itself not >>>>>>>> user-friendly >>>>>>>> or >>>>>>>> rather the way it is incoporated in the portal? >>>>>>>> >>>>>>>> The coordinates in the artemini view differ indeed from the ones >>>>>>>> on >>>>>>>> the >>>>>>>> webpage. this is because the sequence you get to see in the >>>>>>>> artemini >>>>>>>> view >>>>>>>> is only a subpart of the whole scaffold (this in order to let the >>>>>>>> procedure go faster). The coordinates you see in artemini are in >>>>>>>> reference >>>>>>>> to the subpart while you have (and also on the webpage) them in >>>>>>>> reference >>>>>>>> of the whole scaffold. >>>>>>>> >>>>>>>> In theory it is possible to make the coordinates 'box' editable. >>>>>>>> but, >>>>>>>> ... >>>>>>>> i'm a little bit reluctant to do this due to bad experience with >>>>>>>> this >>>>>>>> approach in previous projects. We noticied it is very easy to >>>>>>>> include >>>>>>>> mistakes this way (aspecially for non experienced annotators). >>>>>>>> That >>>>>>>> is >>>>>>>> why >>>>>>>> we include the artemini system in this version (where some basic >>>>>>>> checks >>>>>>>> on >>>>>>>> the structure are performed and you have the visual check of the >>>>>>>> structure). >>>>>>>> But I also completely understand your point that for more >>>>>>>> experienced >>>>>>>> users this might not be ideal... >>>>>>>> What we also can do is to add a function in the artemini to >>>>>>>> 'transfer' >>>>>>>> the >>>>>>>> coordinates you enter (in reference of the whole scaffold) onto >>>>>>>> the >>>>>>>> subpart in artemini. That way you could just paste your >>>>>>>> coordinates >>>>>>>> into >>>>>>>> the coordinate box of artemini, push the 'transfer' button and >>>>>>>> they >>>>>>>> will >>>>>>>> be adjusted onto the subpart. You can then also profit from the >>>>>>>> visual >>>>>>>> check. When you then save your modifications they will be entered >>>>>>>> to >>>>>>>> the >>>>>>>> DB. >>>>>>>> Do you think this might be more useful? or does it still sounds to >>>>>>>> much >>>>>>>> of >>>>>>>> a hastle? >>>>>>>> >>>>>>>> best and thanks for the feedback, >>>>>>>> lieven >>>>>>>> >>>>>>>> >>>>>>>>> Dear Lieven, >>>>>>>>> >>>>>>>>> thanks for the link, I have successfully downloaded the protein >>>>>>>>> database. I would like to start making corrections of the gene >>>>>>>>> models >>>>>>>>> I >>>>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is >>>>>>>> there >>>>>>>> any >>>>>>>> manual how to work with the Artemini tool? I found it not be too >>>>>>>> user-friendly. For instance, I do not understand why the exon >>>>>>>> coordinates indicated by Artemini differs from the actual >>>>>>>> coordinates >>>>>>>> on >>>>>>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>>>>>> coordinates, with an incorrect first exon, are as follows: >>>>>>>>> >>>>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> I would like to change the first exon so that the coordinates are >>>>>>>>> like >>>>>>>> this: >>>>>>>>> >>>>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>>>> >>>>>>>>> The coordinates given for this gene in Artemini are as follows: >>>>>>>>> >>>>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>>>>>> >>>>>>>>> Why there is the difference? I have to say that I would highly >>>>>>>>> appreciate if it is possible to edit gene models just by typing >>>>>>>>> the >>>>>>>> correct coordinates of exons I found by comparing my CDS models >>>>>>>> with >>>>>>>> the >>>>>>>> contig sequence. Is this possible? >>>>>>>>> Thank you and best regards, >>>>>>>>> >>>>>>>>> Marek E. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>> >>>>>>>>>> Dear Marek, >>>>>>>>>> the download is available from this address: >>>>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>>>>>> (login/passw : psbguest/ectocarpus) >>>>>>>>>> Apologises that I haven't informed you earlier, it is quite >>>>>>>>>> hectic >>>>>>>>>> for >>>>>>>> the >>>>>>>>>> moment. >>>>>>>>>> please let me know if this doesn't work. >>>>>>>>>> best regards, >>>>>>>>>> lieven >>>>>>>>>>> Dear Lieven, >>>>>>>>>>> you mentioned that from this week's Monday the whole predicted >>>>>>>> proteome of Ectocarpus should be available for download. I tried >>>>>>>> to >>>>>>>> find >>>>>>>> a >>>>>>>> link to the file at BOGAS web page but haven't found any. Could >>>>>>>> you, >>>>>>>> please, let me know, where to go for the downloading? >>>>>>>>>>> Thanks, best regards, >>>>>>>>>>> Marek Elias >>>>>>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>>>> Dear Marek, >>>>>>>>>>>> From monday on you will be able to download all predicted >>>>>>>>>>>> protein/genes >>>>>>>>>>>> in batch. >>>>>>>>>>>> sorry for the delay. >>>>>>>>>>>> regards, >>>>>>>>>>>> lieven >>>>>>>>>>>> Kenny Billiau wrote: >>>>>>>>>>>>> -------- Original Message -------- >>>>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>>>>>> References: >>>>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>>>>>> Hi Kenny, >>>>>>>>>>>>> thanks for the advice with getting the access to the >>>>>>>>>>>>> Ectocarpus >>>>>>>> portal. I have created an accounted and started to work. Is it >>>>>>>> possible to download the set of predicted protein sequences? It >>>>>>>> would suit me better to do some local stand-alone searches >>>>>>>> (BLAST, >>>>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks >>>>>>>>>>>>> again, >>>>>>>>>>>>> Marek >>>>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>>>>>> login/password. You can use this login to access the ectocarpus >>>>>>>> wiki >>>>>>>>>>>>>> as >>>>>>>>>>>>>> well, >>>>>>>>>>>>>> Kenny >>>>>>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark >>>>>>>>>>>>>>> Cock >>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>>>>>> portal and redirected us to you for obtaining a password >>>>>>>>>>>>>>> to >>>>>>>>>>>>>>> the >>>>>>>> portal. I have one to the BLAST page at the Ghent web site >>>>>>>> (user: ectocarpus, password: sillysilly) but it does not work >>>>>>>> for the portal at >>>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> this >>>>>>>> is not the right link to the portal, so please, let me know how >>>>>>>> can >>>>>>>> I >>>>>>>> access the portal so taht I can start annotating. Thank >>>>>>>> you in advance and best regards, >>>>>>>>>>>>>>> Marek Elias >>>>>>>>>>>>>>> Department of Botany >>>>>>>>>>>>>>> Faculty of Science >>>>>>>>>>>>>>> Charles University >>>>>>>>>>>>>>> Benatska 2 >>>>>>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>>>>>> Czech Republic >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> ================================================================== >>>>>>>> Kenny Billiau >>>>>>>>>>>>>> Web Developer >>>>>>>>>>>>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>>>>>>>>>>>> 3313809 >>>>>>>> VIB Department of Plant Systems Biology, Ghent University >>>>>>>>>>>>>> Technologiepark 927, 9052 Gent, BELGIUM >>>>>>>>>>>>>> kenny.billiau(a)psb.ugent.be >>>>>>>>>>>>>> http://bioinformatics.psb.ugent.be >>>>>>>> ================================================================== >>>>>>>>>>>> -- >>>>>>>>>>>> ============================================================== >>>>>>>>>>>> Lieven >>>>>>>> Sterck Predoctoral fellow Tel:+32 >>>>>>>> (0)9 >>>>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department >>>>>>>> of >>>>>>>> Plant >>>>>>>> Systems Biology, UGent >>>>>>>>>>>> Bioinformatics and Evolutionary Genomics Division >>>>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium >>>>>>>>>>>> Email: >>>>>>>> lieven.sterck(a)psb.ugent.be >>>>>>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>>> Algal >>>>>>>> Genetics Group >>>>>>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>>>>>> VÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©gÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©taux >>>>>>>>>>>> Marins et >>>>>>>>>>>> BiomolÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©cules (Marine >>>>>>>>>>>> Plants and >>>>>>>>>>>> Biomolecules) >>>>>>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>>>>>> 29682 Roscoff Cedex, France >>>>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>>>>>> ============================================================== >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > >

2 1

[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by Lieven Sterck 15 Nov '07

15 Nov '07

Hi Marek, sorry for that! We'll look into it. thanks, lieven > Hi Lieven, > > I am working hard on the annotation but unfortunatelly still some > unexpected problems emerge. Now I face a trouble with annotating the > gene Esi0030_0124. When I insert the correct coordinates, which are as > follows: > > 570185..570280,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 > > However, after I try to save the change to the server, the program > replies with an error message, and when I open the window with the > coordinates, they are changed so that they look like this: > > 2,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975 > > I have not seen this behaviour with other genes, so I have no > explanation for it. What is going on? > > Thanks, > Marek > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> Hi Marek, >> >> This is a not so easy issue (for us! not for you). >> the best option would be to select the model labeled 'CDS' and then >> insert >> your new coordinates. The other models you can ignore. >> >> grtz, >> lieven >> >>> Hi Lieven, >>> >>> thanks for the comments, it now seems that he problem with saving the >>> changes of gene models has been solved. I am sorry, however, to say >>> that I have just encountered another point requiring a discussion with >>> you. I found that some genes I am annotating are incorrectly predicted >>> as two or even three independent loci. How to correct these instances? >>> Should I merge somehow the models into one, which I subsequetly modify >>> bu inserting correct coordinates? If yes, how should I do it? Or >>> should I simply insert the correct coordinates into a field of one of >>> the partial "submodels" and ignore or delete the remaining? >>> Thanks, >>> Marek >>> >>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>> >>>> Hi Marek, >>>> >>>> I spotted the problem. You are talking about locus Esi0425_0013, no? >>>> I can see that you made an edit in the DB, but the problem is that >>>> there >>>> seems to be a double save. If you check in the history the last-1 date >>>> you'll see your edit. >>>> >>>> We are sorting this out as quickly as possible. >>>> >>>> best regards, >>>> lieven >>>> >>>> >>>>> Dear Lieven, >>>>> >>>>> thanks for the change in artemini, this is exactly what I think will >>>>> make the annotation much more straightforward. I checked the system >>>>> with one gene (correcting coordinates of one exon). I saved the >>>>> modified coordinates using "Save to server" command in "File" menu >>>>> option, but the model has not changed in the database yet. Are you >>>>> reviewing opur annotations before incorporating them into the >>>>> database? Or what is going on? >>>>> Thanks. Cheers, >>>>> >>>>> Marek >>>>> >>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>> >>>>>> Dear Marek, >>>>>> >>>>>> we made some adjustments to the artemini functionality and as a >>>>>> result >>>>>> the >>>>>> coordinates you see in the artemini window are now the same as in >>>>>> the >>>>>> webpage (= they are in reference to the whole scaffold). >>>>>> You can just copy and paste your coordinates into the artemini, save >>>>>> it >>>>>> and they will be entered into the DB. >>>>>> >>>>>> I hope this can satisfy your needs. If not, please do let me know, >>>>>> so >>>>>> we >>>>>> can think of better solution. >>>>>> >>>>>> thanks and best regards, >>>>>> lieven >>>>>> >>>>>> >>>>>> ---------------------------- Original Message >>>>>> ---------------------------- >>>>>> Subject: Re: Ectocarpus proteins >>>>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>>>> Date: Thu, November 8, 2007 11:17 pm >>>>>> To: melias(a)natur.cuni.cz >>>>>> Cc: cock(a)sb-roscoff.fr >>>>>> beg-bogas(a)psb.ugent.be >>>>>> -------------------------------------------------------------------------- >>>>>> >>>>>> Dear Marek, >>>>>> >>>>>> You can find a manual on how to use the artemis tool on the Sanger >>>>>> Institute website. >>>>>> May I inquire if you find the artemis tool itself not user-friendly >>>>>> or >>>>>> rather the way it is incoporated in the portal? >>>>>> >>>>>> The coordinates in the artemini view differ indeed from the ones on >>>>>> the >>>>>> webpage. this is because the sequence you get to see in the artemini >>>>>> view >>>>>> is only a subpart of the whole scaffold (this in order to let the >>>>>> procedure go faster). The coordinates you see in artemini are in >>>>>> reference >>>>>> to the subpart while you have (and also on the webpage) them in >>>>>> reference >>>>>> of the whole scaffold. >>>>>> >>>>>> In theory it is possible to make the coordinates 'box' editable. >>>>>> but, >>>>>> ... >>>>>> i'm a little bit reluctant to do this due to bad experience with >>>>>> this >>>>>> approach in previous projects. We noticied it is very easy to >>>>>> include >>>>>> mistakes this way (aspecially for non experienced annotators). That >>>>>> is >>>>>> why >>>>>> we include the artemini system in this version (where some basic >>>>>> checks >>>>>> on >>>>>> the structure are performed and you have the visual check of the >>>>>> structure). >>>>>> But I also completely understand your point that for more >>>>>> experienced >>>>>> users this might not be ideal... >>>>>> What we also can do is to add a function in the artemini to >>>>>> 'transfer' >>>>>> the >>>>>> coordinates you enter (in reference of the whole scaffold) onto the >>>>>> subpart in artemini. That way you could just paste your coordinates >>>>>> into >>>>>> the coordinate box of artemini, push the 'transfer' button and they >>>>>> will >>>>>> be adjusted onto the subpart. You can then also profit from the >>>>>> visual >>>>>> check. When you then save your modifications they will be entered to >>>>>> the >>>>>> DB. >>>>>> Do you think this might be more useful? or does it still sounds to >>>>>> much >>>>>> of >>>>>> a hastle? >>>>>> >>>>>> best and thanks for the feedback, >>>>>> lieven >>>>>> >>>>>> >>>>>>> Dear Lieven, >>>>>>> >>>>>>> thanks for the link, I have successfully downloaded the protein >>>>>>> database. I would like to start making corrections of the gene >>>>>>> models >>>>>>> I >>>>>> foud to be incorrectly predicted ion the rpesent annotation. Is >>>>>> there >>>>>> any >>>>>> manual how to work with the Artemini tool? I found it not be too >>>>>> user-friendly. For instance, I do not understand why the exon >>>>>> coordinates indicated by Artemini differs from the actual >>>>>> coordinates >>>>>> on >>>>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>>>> coordinates, with an incorrect first exon, are as follows: >>>>>>> >>>>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>> >>>>>>> I would like to change the first exon so that the coordinates are >>>>>>> like >>>>>> this: >>>>>>> >>>>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>>>> >>>>>>> The coordinates given for this gene in Artemini are as follows: >>>>>>> >>>>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>>>> >>>>>>> Why there is the difference? I have to say that I would highly >>>>>>> appreciate if it is possible to edit gene models just by typing the >>>>>> correct coordinates of exons I found by comparing my CDS models with >>>>>> the >>>>>> contig sequence. Is this possible? >>>>>>> Thank you and best regards, >>>>>>> >>>>>>> Marek E. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>> >>>>>>>> Dear Marek, >>>>>>>> the download is available from this address: >>>>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>>>> (login/passw : psbguest/ectocarpus) >>>>>>>> Apologises that I haven't informed you earlier, it is quite hectic >>>>>>>> for >>>>>> the >>>>>>>> moment. >>>>>>>> please let me know if this doesn't work. >>>>>>>> best regards, >>>>>>>> lieven >>>>>>>>> Dear Lieven, >>>>>>>>> you mentioned that from this week's Monday the whole predicted >>>>>> proteome of Ectocarpus should be available for download. I tried to >>>>>> find >>>>>> a >>>>>> link to the file at BOGAS web page but haven't found any. Could you, >>>>>> please, let me know, where to go for the downloading? >>>>>>>>> Thanks, best regards, >>>>>>>>> Marek Elias >>>>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>>>> Dear Marek, >>>>>>>>>> From monday on you will be able to download all predicted >>>>>>>>>> protein/genes >>>>>>>>>> in batch. >>>>>>>>>> sorry for the delay. >>>>>>>>>> regards, >>>>>>>>>> lieven >>>>>>>>>> Kenny Billiau wrote: >>>>>>>>>>> -------- Original Message -------- >>>>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>>>> References: >>>>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>>>> Hi Kenny, >>>>>>>>>>> thanks for the advice with getting the access to the Ectocarpus >>>>>> portal. I have created an accounted and started to work. Is it >>>>>> possible to download the set of predicted protein sequences? It >>>>>> would suit me better to do some local stand-alone searches (BLAST, >>>>>>>>>>> HMMER) than to use only your web BLAST server. Thanks again, >>>>>>>>>>> Marek >>>>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>>>> Hi, >>>>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>>>> login/password. You can use this login to access the ectocarpus >>>>>> wiki >>>>>>>>>>>> as >>>>>>>>>>>> well, >>>>>>>>>>>> Kenny >>>>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark Cock >>>>>>>>>>>>> sent >>>>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>>>> portal and redirected us to you for obtaining a password to >>>>>>>>>>>>> the >>>>>> portal. I have one to the BLAST page at the Ghent web site >>>>>> (user: ectocarpus, password: sillysilly) but it does not work >>>>>> for the portal at >>>>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May be >>>>>>>>>>>>> this >>>>>> is not the right link to the portal, so please, let me know how >>>>>> can >>>>>> I >>>>>> access the portal so taht I can start annotating. Thank >>>>>> you in advance and best regards, >>>>>>>>>>>>> Marek Elias >>>>>>>>>>>>> Department of Botany >>>>>>>>>>>>> Faculty of Science >>>>>>>>>>>>> Charles University >>>>>>>>>>>>> Benatska 2 >>>>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>>>> Czech Republic >>>>>>>>>>>> -- >>>>>>>>>>>> ================================================================== >>>>>> Kenny Billiau >>>>>>>>>>>> Web Developer >>>>>>>>>>>> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 >>>>>>>>>>>> 3313809 >>>>>> VIB Department of Plant Systems Biology, Ghent University >>>>>>>>>>>> Technologiepark 927, 9052 Gent, BELGIUM >>>>>>>>>>>> kenny.billiau(a)psb.ugent.be >>>>>>>>>>>> http://bioinformatics.psb.ugent.be >>>>>> ================================================================== >>>>>>>>>> -- >>>>>>>>>> ============================================================== >>>>>>>>>> Lieven >>>>>> Sterck Predoctoral fellow Tel:+32 (0)9 >>>>>> 3313821 Fax:+32 (0)9 3313809 VIB Department of >>>>>> Plant >>>>>> Systems Biology, UGent >>>>>>>>>> Bioinformatics and Evolutionary Genomics Division >>>>>>>>>> Technologiepark 927, B-9052 Gent, Belgium >>>>>>>>>> Email: >>>>>> lieven.sterck(a)psb.ugent.be >>>>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> Algal >>>>>> Genetics Group >>>>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>>>> VÃÂÃÂÃÂÃÂ©gÃÂÃÂÃÂÃÂ©taux Marins et >>>>>>>>>> BiomolÃÂÃÂÃÂÃÂ©cules (Marine >>>>>>>>>> Plants and >>>>>>>>>> Biomolecules) >>>>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>>>> 29682 Roscoff Cedex, France >>>>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>>>> ============================================================== >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > >

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Re: [Beg-bogas] Getting started with BOGAS
by Thomas Abeel 15 Nov '07

15 Nov '07

Hello again, If you get the same error for both programs, it has probably something to do with the configuration of Java Web Start or your computer. From your error I have the impression that it has something to with you network connection. Please make sure that your firewall allows traffic from Java to load the required jar files. Can you get more information about the error? Artemini was tested both with Java 1.5 and 1.6, so the version should be no problem. kind regards, Thomas Claire Gachon schreef: > Hi Thomas, > thanks for your swift answer. > > 1) View alignment: I don't know what goes wrong, but I tried again > with Esi0009_0001 and Esi0009_0004: I just get this message > > 2) I have now tried Artemini, and it gives me the same kind of error > message as above > An error occurred while launching/running the application. > > Title: Artemini: Genome Visualization and Annotation > Vendor: VIB :: Plant Systems Biology :: Bioinformatics :: Thomas Abeel > Category: Download Error > > Unable to load resource: > http://bioinformatics.psb.ugent.be/webtools/artemini/artemini-2.11.jar > > > Could it be that somethign is wrong with my version of Java Web start? > > Claire > > At 15:07 15/11/2007, you wrote: >> Hello Claire, >> >>> _1) View alignment:_ when I click on the button, >>> Java web Start gets launched, "Checking for latest version" >>> then I get this message: >>> >>> Java Web start: Download Error >>> Unable to launch AlignView: a Sequence Alignment Viewer. >>> >>> Details: >>> An error occurred while launching/running the application. >>> >>> Title: AlignView: A Sequence Alignment Viewer >>> Vendor: VIB :: Plant Systems Biology :: Thomas Abeel >>> Category: Download Error >>> >>> Unable to load resource: >>> http://bioinformatics.psb.ugent.be/webtools/alignview/alignview-0.6.jar >> Which steps should I take to reproduce this error? I have just now >> tried to view the aligment for Esi0009_0001 and I encountered no >> problems. >> >> >>> _2) ESTs: >>> _EST is incompatible with the predicted model: is there any way to >>> retrieve easily ESTs sequences from the annotation page, in order to >>> check what is wrong with them (or the gene prediction? >>> Should I do it with Artemis (see below)? >>> >>> _3) Artemis_: >>> I have tried to install it on my computer (PC with Windows). So far >>> I have downloaded the file artemis.jar. My Java version is 1.5.0_08 >>> When I double-click on it, I get the following message: >>> Java Virtual Machine Launcher : Invalid or corrupt jar file >>> c:\Program files\artemis.jar >>> >>> Can you help? >> >> You should not download the artemis.jar file. The Artemis version >> within the BOGAS platform, called Artemini, is modified from the >> original Artemis program. This is again a Java Webstart Application. >> To launch Artemini for a locus, you can select 'Modify using >> Artemini' under the header 'Gene Structure' on the page that shows >> after you click the 'Modify This record' button. >> >> kind regards, >> Thomas

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[Fwd: Re: [Beg-bogas] Re: BOGAS]
by Lieven Sterck 15 Nov '07

15 Nov '07

---------------------------- Original Message ---------------------------- Subject: Re: [Beg-bogas] Re: BOGAS From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> Date: Thu, November 15, 2007 6:37 pm To: "Patrice Lerouge" <Patrice.Lerouge(a)univ-rouen.fr> -------------------------------------------------------------------------- Dear Patrice, what do you mean with 'access to data' ?? If you are able to login on the website, you should have access to all the data. kind regards, lieven > OK for entering in the website but it seems that I need a password for > having access to data. > Best regards > Patrice LEROUGE > > > > > A 11:09 14/11/2007 +0100, vous avez écrit : >>Hi, >> >>you have been invited to take part in the annotation of Ectoca= rpus. >>Please click on following link to activate your user account: >> >><3d'http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitatio>f4f58da406d3cccacae >>2a9ee547e5474 >> >>If the link doesn't work, try to go to http://bi= >>oinformatics.psb.ugent.be/webtools/bogas/users/enteric and enter >>f4f58da406d3cccacae2a9ee547e5474 >> >>with kind regards, >>t= he BOGAS team > _______________________________________________ > Beg-bogas mailing list > Beg-bogas(a)psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas >

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[Beg-bogas] trpee kapot
by Thomas Abeel 15 Nov '07

15 Nov '07

Ik krijg voor elke locus van Trpee non-existant locus. groeten, Thomas

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