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

[Beg-bogas] Re: BOGAS
by kjabbari＠infobiogen.fr 20 Dec '07

20 Dec '07

Thank you beg-bogas, now it is ok. kamel > > Please go to following link > http://bioinformatics.psb.ugent.be/webtools/bogas/users/reenterpassword/8= > 1e8602d82ab5ef33c0b1d7a87fa675c Or you can enter > the code manually on http://bioinformatics.psb.ugent.be/webtools/bogas/us= > ers/reenterpasswordtoken > : 81e8602d82ab5ef33c0b1d7a87fa675c After you log in with th= > is password, please change it to something you can > remember! >

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[Beg-bogas] Re: BOGAS IDpass
by kjabbari＠infobiogen.fr 20 Dec '07

20 Dec '07

Dear webmaster, Thanks for answering so fast, unfortunately, the "typos" that came with your e-mail are hard to follow, in fact the absence of spaces made the adress: http.... long and unreadable to me, could you please clarify this, may be some thing like: ID is: Pass is: Thank you again and sorry for the bother Dr. Kamel Jabbari > > Please go to following link > http://bioinformatics.psb.ugent.be/webtools/bogas/users/reenterpassword/8= > 1e8602d82ab5ef33c0b1d7a87fa675c Or you can enter > the code manually on http://bioinformatics.psb.ugent.be/webtools/bogas/us= > ers/reenterpasswordtoken > : 81e8602d82ab5ef33c0b1d7a87fa675c After you log in with th= > is password, please change it to something you can > remember! >

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[Beg-bogas] invitation into the annotation of E. siliculosus
by Andres Ritter 20 Dec '07

20 Dec '07

hello, My name is Andres Ritter, I make part of the annotation consortium, so if it's possible, I would like to obtain a username and a password. My best regards, -- Andrés Ritter PhD student Algal Defense group, UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique, Place Georges Teissier, BP74 29682 Roscoff Cedex, France Tel: 33.2.98.29.23.23, Fax: 33.2.98.29.23.24 Email: ritter(a)sb-roscoff.fr http://www.sb-roscoff.fr/UMR7139

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[Beg-bogas] [Fwd: Re: [Fwd: Re: Ectocarpus proteins]]
by Lieven Sterck 19 Dec '07

19 Dec '07

---------------------------- Original Message ---------------------------- Subject: Re: [Fwd: Re: Ectocarpus proteins] From: melias(a)natur.cuni.cz Date: Tue, December 18, 2007 10:11 pm To: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> -------------------------------------------------------------------------- Hi Lieven, the Czech error page reports something like this "The page cannot be found". M. Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > Hi Marek, > > We'll look into it. > any possibility you can give us (preferably the english translation ;-) > )the czech error message? > > thx, > lieven > >> Hil Lieven, >> >> I would like to place some text on "my" page in the Ectocarpus Wiki >> site (the link "G Proteins" on the main page). When I put the text >> into the window (invoked by pressing "Create this page") and press >> "Save", teh browser swithc to a page with a Czech error report, whcih >> after reloding changes to a page sayin "Sorry, you don't have enough >> rights to continue. Perhaps you forgot to login?". However, I am >> logged. Could you, please, look at this problem? >> Thanks, >> Marek >> >> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >> >>> Hi Marek, >>> >>> I fear you just demonstrated why we use the artemini as a check (in >>> stead of making the coordinate box on the webpage editable) :-[ : >>> there is an error in the coordinate set you provide: >>> ...... >>> ,439639..439695,440076..440186,440581..440670,441533..441669,4422224..442297,442889......... >>> artemini complains because the seq is only ~1.2Mb long and your >>> coordinate is ~4.4Mb . >>> >>> grtz, >>> lieven >>> >>> >>> melias(a)natur.cuni.cz wrote: >>>> Hi Lieven, >>>> >>>> it seems that you indeed partially solved the problem with saving >>>> exon coordinates as I now could save the coordinates of the gene >>>> Esi0031_0121 using the pption 'Modify Using Artemini (full >>>> sequence)'. However, even this option does not work for the gene >>>> Esi0008_0081, which should actually be merged with the gene >>>> Esi0008_0082 so that the coordinates should be as follows: >>>> >>>> 435416..436165,437250..437506,437809..437896,438082..438272,438896..439229,439639..439695,440076..440186,440581..440670,441533..441669,4422224..442297,442889..442998,443534..443650,444305..444505,445069..445218,445540..445680,446186..446371,447092..447184 >>>> The error message is still the same - it is out of the range of the >>>> sequence. Could you, please, have a look on >>>> this? >>>> thanks, >>>> Marek >>>> >>>> >>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>> >>>>> 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 >>>>>>>>>>>>>>>>>>> VÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©gÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©taux >>>>>>>>>>>>>>>>>>> Marins >>>>>>>>>>>>>>>>>>> et >>>>>>>>>>>>>>>>>>> BiomolÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂ©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 >>>>> VÃÂ©gÃÂ©taux Marins et BiomolÃÂ©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 >>> VÃÂ©gÃÂ©taux Marins et BiomolÃÂ©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 18 Dec '07

18 Dec '07

-------- Original Message -------- Subject: Re: [Fwd: Re: Ectocarpus proteins] Date: Tue, 18 Dec 2007 18:36:01 +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> <20071127111303.awlb688t4wc0osck(a)www.natur.cuni.cz> <474EDB0F.2070506(a)psb.ugent.be> <20071209190956.o98l3ufc0g840wc0(a)www.natur.cuni.cz> <475D1A60.7040101(a)psb.ugent.be> Hil Lieven, I would like to place some text on "my" page in the Ectocarpus Wiki site (the link "G Proteins" on the main page). When I put the text into the window (invoked by pressing "Create this page") and press "Save", teh browser swithc to a page with a Czech error report, whcih after reloding changes to a page sayin "Sorry, you don't have enough rights to continue. Perhaps you forgot to login?". However, I am logged. Could you, please, look at this problem? Thanks, Marek Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: > Hi Marek, > > I fear you just demonstrated why we use the artemini as a check (in > stead of making the coordinate box on the webpage editable) :-[ : > there is an error in the coordinate set you provide: > ...... > ,439639..439695,440076..440186,440581..440670,441533..441669,4422224..442297,442889......... > artemini complains because the seq is only ~1.2Mb long and your > coordinate is ~4.4Mb . > > grtz, > lieven > > > melias(a)natur.cuni.cz wrote: >> Hi Lieven, >> >> it seems that you indeed partially solved the problem with saving >> exon coordinates as I now could save the coordinates of the gene >> Esi0031_0121 using the pption 'Modify Using Artemini (full >> sequence)'. However, even this option does not work for the gene >> Esi0008_0081, which should actually be merged with the gene >> Esi0008_0082 so that the coordinates should be as follows: >> >> 435416..436165,437250..437506,437809..437896,438082..438272,438896..439229,439639..439695,440076..440186,440581..440670,441533..441669,4422224..442297,442889..442998,443534..443650,444305..444505,445069..445218,445540..445680,446186..446371,447092..447184 The error message is still the same - it is out of the range of the sequence. Could you, please, have a look on >> this? >> thanks, >> Marek >> >> >> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >> >>> 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. Itis >>>>> 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 asin >>>>>>>>>>>>> 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 >>> ============================================================== >> > > -- > ============================================================== > 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 > ============================================================== -- ============================================================== 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 ==============================================================

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[Beg-bogas] bogas account
by lieven sterck 14 Dec '07

14 Dec '07

Dear Ludovic, if you copy paste the following address in your browser you should get there: http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitationcode/3dd6… kind regards, lieven -- ============================================================== 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 ==============================================================

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[Beg-bogas] Re: BOGAS
by Ludovic Delage 14 Dec '07

14 Dec '07

Hi, I have tried the links you gave me but none of them works. What can I do ? Best regards >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>53f20a691f37a601b0c >1fea61b6338c5 > >If the link doesn't work, try to go to http://bi= >oinformatics.psb.ugent.be/webtools/bogas/users/enteric and enter >53f20a691f37a601b0c1fea61b6338c5 > >with kind regards, >t= he BOGAS team

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[Beg-bogas] schouderklopke
by Lieven Sterck 14 Dec '07

14 Dec '07

After all the bugs/errors/probs here a positive comment, acknowledging our hard work: " Thanks again, and thanks also for all the work which you're putting into this! " (from JHB) and another one (more for myself ;-) ): "If it is any consolation, I have the impression that the Ectocarpus gene models are pretty good, despite such errors. We had a look at Ehux earlier on in the week here in Roscoff and those predictions are a real mess." (from MC) (And I/we should be able to do even better ;-) ) Well done!! keep up the good work! L.

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[Beg-bogas] Fwd: Re: Bogas annotator
by Ludovic Delage 12 Dec '07

12 Dec '07

Hello, Could I have a password to annotate some Ectocarpus genes please. Thanks >X-Sieve: CMU Sieve 2.2 >Date: Wed, 12 Dec 2007 14:34:41 +0100 >From: Mark Cock <cock(a)sb-roscoff.fr> >User-Agent: Thunderbird 2.0.0.9 (Macintosh/20071031) >To: Ludovic Delage <delage(a)sb-roscoff.fr> >CC: Bernhard Gschloessl <gschloessl(a)sb-roscoff.fr>, > lieven sterck <lieven.sterck(a)psb.ugent.be>, > Kenny Billiau <kenny.billiau(a)psb.ugent.be> >Subject: Re: Bogas annotator >X-Virus-Scanned: amavisd-new at gamel.sb-roscoff.fr > >Hi Ludo, > >No problem if you want to do some annotation. Philippe has signed up for >quite a number of gene families and pathways (Defence genes, halide >metabolism, oxidative stress, secondary metabolism (phlorotannins, CHS, >CHI, etc), proteomics). All the information is in the two attached files. >Just send a mail to beg-bogas(a)psb.ugent.be asking for a password. > >Mark > > > >Best regards, > >Mark

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[Beg-bogas] access to Bogas
by Susana Coelho 12 Dec '07

12 Dec '07

Hi, I would like to have access to the Ectocarpus annotation system.... Thanks Susana

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