November 2007 - beg-bogas@psb.ugent.be

[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by lieven sterck 29 Nov '07

29 Nov '07

Hi Marek, We solved this the following way: You now have a choice between 2 possible downloads in artemini: small sequence (as it was) and the whole sequence ('Modify Using Artemini (full sequence)' ). With the whoel sequence you should have the problem anymore (but it can take longer to download it). grtz, lieven melias(a)natur.cuni.cz wrote: > Hi Lieven, > > I onece more cannot save coordinates of a gene moeld edited in Artemini. > I need to save the following coordinates for the gene Esi0031_0121: > > 650149..650208,650956..651132,651761..651904,652788..652932,653394..653455,654128..654328,654791..654934,655760..655847,662896..663023,663661..663789,664631..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510 > > > When I put them to the respective widow and press "OK", the following > error announcement appears: > > Cannot apply changes because of location error: Parse error at this > point: > ..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510)): > garbage at the end of the location string > > Could you, please, have a look on this? > > Thanks, > Marek > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> 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 >>>>>>>>>>>>>> ============================================================== >>>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > -- ============================================================== 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 Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

1 0

[Beg-bogas] Esi0011_0004 kapot
by Thomas Abeel 28 Nov '07

28 Nov '07

Esi0011_0004 Offset:1849 FT CDS_before join(complement(745..1152),complement(1791..1878), FT CDS_before join(complement(3190..3358),complement(4684..4814)) FT CDS_after join(16108..16247,16956..17106,17921..18054,18654..18753, FT CDS_after join(complement(26734..26889)) FT CDS join(complement(7438..7452),complement(8122..8286), ... FT BLASTN_HIT join(complement(61227..61633),complement(61756..61760), FT BLASTN_HIT complement(61316..61518) FT BLASTN_HIT complement(61227..61633) ... SQ Sequence 27479 BP; 6285 A; 7148 C; 7231 G; 5839 T; 976 other; Het is duidelijk dat die BLASTN_HITS nog niet in de buurt komen om in die sequentie te vallen. Twee mogelijke oplossingen: - Die BLASTN_HITS worden niet in de EMBL gestoken - Ik pas Artemini aan zodat features die niet binnen de sequentie passen, gewoon worden weggelaten. groeten Thomas

1 1

[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by lieven sterck 27 Nov '07

27 Nov '07

Hi Marek, The 'problem' is that you are entering coordinates that extend the region we sent over for artemini (we use a contest of 2 genes up and downstream). That worked fine for most cases but apparently for some this is not enough yet. Therefore we are now working on an update that will allow you to retrieve the complete scaffold, which should solve your problem. sorry for the inconvenience, grtz, lieven melias(a)natur.cuni.cz wrote: > Hi Lieven, > > I onece more cannot save coordinates of a gene moeld edited in Artemini. > I need to save the following coordinates for the gene Esi0031_0121: > > 650149..650208,650956..651132,651761..651904,652788..652932,653394..653455,654128..654328,654791..654934,655760..655847,662896..663023,663661..663789,664631..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510 > > > When I put them to the respective widow and press "OK", the following > error announcement appears: > > Cannot apply changes because of location error: Parse error at this > point: > ..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510)): > garbage at the end of the location string > > Could you, please, have a look on this? > > Thanks, > Marek > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> 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 >>>>>>>>>>>>>> ============================================================== >>>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > -- ============================================================== 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 Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

1 0

Re: [Beg-bogas] Error communicating with the database
by lieven sterck 27 Nov '07

27 Nov '07

Hi Claire, there seems to be a mix-up with the URLs! the one and only webaddress you have to remember (and bookmark) is : http://bioinformatics.psb.ugent.be/webtools/bogas Did you already made lost of annotations via this webaddress? grtz, lieven Claire Gachon wrote: > Hi Lieven, > > I have used my usual bookmark > http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/BOGAS/trunk/www/s… > > logged in, and have had the problem. > > As for how I got the bookmark in the first place, I must have used the > address you gave us in Evry, and bookmarked the login page. > > I did not (consciously) do anything special: I would not describe > myself as a genius hacker ;) > sorry, I can't help more. > > Claire > > > At 22:57 26/11/2007, you wrote: >> Hi Claire, >> >> Could you perhaps tell us what you did / how you came to this 'wrong' >> web-address? >> >> also the production site can be found at: >> http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/.... >> >> (when it says 'sandbox' in the url it's the production site. >> >> sorry for the inconvenience, >> best regards, >> lieven >> >> >> > Hi Claire, >> > >> > for one reason or another you've stumbled upon the development version >> > of the BOGAS website. >> > After you've logged in, you should try this url: >> > >> http://bioinformatics.psb.ugent.be/webtools/bogas/annotation/Ectsi/666666/E… >> >> > Which should lead you to the locus you were about the access. >> > >> > The production version of the website can be found on: >> > http://bioinformatics.psb.ugent.be/webtools/bogas >> > >> > kind regards, >> > Kenny >> > >> > lieven sterck wrote: >> >> Hi Claire, >> >> >> >> yes, I know, apologies for that! >> >> Best is to wait a little bit because we are working on it.. >> >> >> >> thanks, >> >> lieven >> >> >> >> >> >> Claire Gachon wrote: >> >>> Hi, >> >>> I have difficulties accessing the Ectocarpus loci (although the >> Blast >> >>> function works). >> >>> what ever the locus I am searchig for, I get the following error >> >>> message: >> >>> >> >>> Error communicating with the database. Please contact the webmaster >> >>> with the details if the error. >> >>> url, genome, release, locus >> >>> DBD::mysql::st execute failed: Table 'bogas_ectsi_v2.history' >> doesn't >> >>> exist at ../../src/perl/modules//BOGAS/AnnotDB.pm line 453. >> >>> >> >>> >> http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/BOGAS/trunk/www/s… >> >> >>> >> >>> >> >>> what should I do? >> >>> thanks in advance >> >>> Claire >> > -- >> > ================================================================== >> > 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 >> > ================================================================== >> > > > > Dr Claire GACHON > Scottish Association for Marine Science > Dunstaffnage Marine Laboratory > PA37 1QA Oban > United Kingdom > claire.gachon(a)sams.ac.uk > Tel: 0044 16 31 559 318 > Fax 0044 16 31 559 001 > http://www.sams.ac.uk/ > http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-… > > > +++++++++++++++++++++++++++++++ > The Scottish Association for Marine Science (SAMS) is registered in > Scotland as a Company Limited by Guarantee (SC009292) and is a > registered charity (9206). There are 2 wholly owned subsidiary > companies: SAMS Research Services Ltd a Limited Company (SC224404) and > the European Centre for Marine Biotechnology, a Company Limited By > Guarantee (SC205318). All Companies in the group are registered in > Scotland and share a registered office at Dunstaffnage Marine > Laboratory, Oban Argyll PA37 1QA. > > The content of this message may contain personal views which are not > the views of SAMS unless specifically stated. > > Please note that all email traffic is monitored for purposes of > security and spam filtering. As such individual emails may be examined > in more detail. > +++++++++++++++++++++++++++++++ -- ============================================================== 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 Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

1 0

[Beg-bogas] [Fwd: Re: [Fwd: Re: Ectocarpus proteins]]
by lieven sterck 27 Nov '07

27 Nov '07

bij u thabe of bij mij??? L. -------- Original Message -------- Subject: Re: [Fwd: Re: Ectocarpus proteins] Date: Tue, 27 Nov 2007 11:13:03 +0100 From: melias(a)natur.cuni.cz To: Lieven Sterck <lieven.sterck(a)psb.ugent.be> References: <58246.157.193.202.129.1194749039.squirrel(a)webmail.psb.ugent.be> <20071113111523.7qanxvnt3t4zggcg(a)www.natur.cuni.cz> <35316.157.193.202.129.1194998042.squirrel(a)webmail.psb.ugent.be> <20071114191407.oj2lemhpebegw00s(a)www.natur.cuni.cz> <44719.157.193.202.129.1195088065.squirrel(a)webmail.psb.ugent.be> <20071115162254.65qzjhw4ihw04s0g(a)www.natur.cuni.cz> <53689.157.193.202.129.1195164829.squirrel(a)webmail.psb.ugent.be> <20071116221047.oekxk8bj8668wgk4(a)www.natur.cuni.cz> <15272.157.193.202.129.1195254098.squirrel(a)webmail.psb.ugent.be> Hi Lieven, I onece more cannot save coordinates of a gene moeld edited in Artemini. I need to save the following coordinates for the gene Esi0031_0121: 650149..650208,650956..651132,651761..651904,652788..652932,653394..653455,654128..654328,654791..654934,655760..655847,662896..663023,663661..663789,664631..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510 When I put them to the respective widow and press "OK", the following error announcement appears: Cannot apply changes because of location error: Parse error at this point: ..664729,665569..665796,666203..666318,666898..667006,667469..667526,668411..668577,669887..670197,670893..670998,672023..672127,672633..672761,673309..673461,674180..674335,675415..675510)): garbage at the end of the location string Could you, please, have a look on this? Thanks, Marek Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > 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 >>>>>>>>>>>>> ============================================================== >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > > -- ============================================================== 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 Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

1 0

[Fwd: Re: [Beg-bogas] Error communicating with the database]
by lieven sterck 27 Nov '07

27 Nov '07

da verklaard... L. -------- Original Message -------- Subject: Re: [Beg-bogas] Error communicating with the database Date: Tue, 27 Nov 2007 10:37:09 +0000 From: Claire Gachon <claire.gachon(a)sams.ac.uk> To: Lieven Sterck <lieven.sterck(a)psb.ugent.be> References: <7.0.1.0.1.20071126152245.01b06d60(a)sams.ac.uk> <474AED62.4000400(a)psb.ugent.be> <474B1C8D.6040003(a)psb.ugent.be> <37931.157.193.202.129.1196117828.squirrel(a)webmail.psb.ugent.be> Hi Lieven, I have used my usual bookmark http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/BOGAS/trunk/www/s… logged in, and have had the problem. As for how I got the bookmark in the first place, I must have used the address you gave us in Evry, and bookmarked the login page. I did not (consciously) do anything special: I would not describe myself as a genius hacker ;) sorry, I can't help more. Claire At 22:57 26/11/2007, you wrote: >Hi Claire, > >Could you perhaps tell us what you did / how you came to this 'wrong' >web-address? > >also the production site can be found at: >http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/.... > >(when it says 'sandbox' in the url it's the production site. > >sorry for the inconvenience, >best regards, >lieven > > > > Hi Claire, > > > > for one reason or another you've stumbled upon the development version > > of the BOGAS website. > > After you've logged in, you should try this url: > > > http://bioinformatics.psb.ugent.be/webtools/bogas/annotation/Ectsi/666666/E… > > Which should lead you to the locus you were about the access. > > > > The production version of the website can be found on: > > http://bioinformatics.psb.ugent.be/webtools/bogas > > > > kind regards, > > Kenny > > > > lieven sterck wrote: > >> Hi Claire, > >> > >> yes, I know, apologies for that! > >> Best is to wait a little bit because we are working on it.. > >> > >> thanks, > >> lieven > >> > >> > >> Claire Gachon wrote: > >>> Hi, > >>> I have difficulties accessing the Ectocarpus loci (although the Blast > >>> function works). > >>> what ever the locus I am searchig for, I get the following error > >>> message: > >>> > >>> Error communicating with the database. Please contact the webmaster > >>> with the details if the error. > >>> url, genome, release, locus > >>> DBD::mysql::st execute failed: Table 'bogas_ectsi_v2.history' doesn't > >>> exist at ../../src/perl/modules//BOGAS/AnnotDB.pm line 453. > >>> > >>> > http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/BOGAS/trunk/www/s… > >>> > >>> > >>> what should I do? > >>> thanks in advance > >>> Claire > > -- > > ================================================================== > > 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 > > ================================================================== > > Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon(a)sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-… +++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA. The content of this message may contain personal views which are not the views of SAMS unless specifically stated. Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++ -- ============================================================== 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 Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

1 0

[Beg-bogas] Error communicating with the database
by Claire Gachon 26 Nov '07

26 Nov '07

Hi, I have difficulties accessing the Ectocarpus loci (although the Blast function works). what ever the locus I am searchig for, I get the following error message: Error communicating with the database. Please contact the webmaster with the details if the error. url, genome, release, locus DBD::mysql::st execute failed: Table 'bogas_ectsi_v2.history' doesn't exist at ../../src/perl/modules//BOGAS/AnnotDB.pm line 453. http://bioinformatics.psb.ugent.be/webtools/sandbox/liste/BOGAS/trunk/www/s… what should I do? thanks in advance Claire Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon(a)sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-… +++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA. The content of this message may contain personal views which are not the views of SAMS unless specifically stated. Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++

4 3

[Beg-bogas] Re: Bogas
by Lieven Sterck 25 Nov '07

25 Nov '07

Hi Mark, > Hi Lieven, > > A couple of other things: > > I have created a page on the wifi where people can note bacterial > contaminants. Is this OK? Sure, no problem! That why it's there for. I think that there was already one in the assembly problems section? > > Did you try to remove the php extension from the Artemis and alignment > files? It is pain having to reconfigure them each time and my computer > won't accept the command to "open all files like this with Java web start" I'm sorry, I thought this was already fixed :-[ ! I'll add it again to the list of things (urgently) to be done. grtz, lieven > > Thanks, > > Mark >

1 0

[Beg-bogas] Getting started with BOGAS
by Claire Gachon 20 Nov '07

20 Nov '07

Hi, I have just been trying to annotate my first Ectocarpus gene (Esi0009_0001). And of course, I am struggling with the most basic functions: 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 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? Thanks a lot in advance, Claire Dr Claire GACHON Scottish Association for Marine Science Dunstaffnage Marine Laboratory PA37 1QA Oban United Kingdom claire.gachon(a)sams.ac.uk Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/ http://www.sams.ac.uk/research/departments/microbial-molecular/mmb-project-… +++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). There are 2 wholly owned subsidiary companies: SAMS Research Services Ltd a Limited Company (SC224404) and the European Centre for Marine Biotechnology, a Company Limited By Guarantee (SC205318). All Companies in the group are registered in Scotland and share a registered office at Dunstaffnage Marine Laboratory, Oban Argyll PA37 1QA. The content of this message may contain personal views which are not the views of SAMS unless specifically stated. Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail. +++++++++++++++++++++++++++++++

4 5

[Beg-bogas] Esi0011_0005 messed up layout
by Thomas Abeel 20 Nov '07

20 Nov '07

Esi0011_0005 has a messed up layout on its webpage, as far as I can see this is caused by a very long structure 17957..18096,18805..18955,19770..19903,20503..20602,21306..21440,22429..22533,23272..23413,23986..24130,24374..24544,25101..25332,25864..25951,26381..26456,26969..270... This occurs with multiple loci that have a similarly long or even longer structure. The last part of the structure also disappears under the moving menu on the right side. regards, Thomas

1 0