-------- Original Message -------- Subject: Re: Stefan ... & BOGAS (2) Date: Tue, 08 Jan 2008 09:54:29 +0100 From: Pierre Rouze <pirou@psb.UGent.be> To: Lieven Sterck <lieven.sterck@psb.ugent.be> References: <477F3B8A.4090704@psb.UGent.be> <19271.157.193.202.129.1199536388.squirrel@webmail.psb.ugent.be> <477FCB57.8020606@psb.UGent.be> <4781EF18.40908@psb.ugent.be> <47826356.9050303@psb.UGent.be> <51222.157.193.202.129.1199747946.squirrel@webmail.psb.ugent.be> Lieven Sterck wrote: Artemini is too mini : there is no way to create features besides CDS !!! I need it myself (eg, to map repeats, NNN, introns, etc ...): what shall I do ?

Hi Pierre,

with 'edit' I mean the 'Modify This Record' button. Clicking on that will lead you to the 'edit page'.

I don't see what you mention about the links, they all work with me! Also the workbench is working fine. I can see that you added the locus Esi0000_0035 on your workbench, I cannot edit ;-) it for the moment.

more tomorrow. grtz, lieven

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lieven sterck wrote:

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Hi Pierre,

the artemis interface is available. Therefore you have to go to the edit page and in the gene-structure section you will then find link(s) to artemini.

Sorry, but I spent already an hour with this Bogus, without seing any "Edit" or whatever alike offered to me:

first page : Ostreoccus versus Ectocarpus : not too difficult this one : I chose Ectocarpus

second page, already more difficult : Annotation, Browse (it would have been my choice, but it is inactive..) Blast, Search & Wiki OK I got for search and got the first sequence in the list, Esi0000_0035 by entering it in the Locus window.. Then I understood that I add to choose either View or Workbench... Workbench has no effect but to put the gene on it !!! (is this button useful, really???) Then View, with a nice navigation menu on the right... at least that's what I thought : looking for your gene in detail whith the next one will be here, sure . No way ! No Edit or Artemini either.. In fact, it's mosty shortcuts to things which I could have done before (search, workbench) or infos already displayed on the screen... Exception : Previous & New locus, but you end up with the very same stuff (for the neighbour gene..), Blast: OK. Add to : same effect as the unuseful workbench button ....

And nothing else !!!!

So, where damned is that "edit" page ??? It should be one pop-up in the very first screen, immediately after you accessed a gene ! No one complained about it ?

For the protein alignment do you mean that you can not 'click' on a gene in the alignment viewer?

I mean, clicking on the "green looking" Genbank entry name with is displayed on the line "Protein ID: .." BELOW the button "protein alignment" : there is nothing coming up, when one (me at least) would expect this to be an active link to the Genbank entry, allowing to check what is this protein for real ... It's the same if you open the Blast display by clicking "View Blast" : it's all dead info, no active link...

P.

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grtz, lieven

Pierre Rouze wrote:

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Lieven Sterck wrote:

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Hi Pierre,

it looks like you are accessing the wrong 'BOGAS'. Does the website you visit has an URL like .../sandbox/liste/BOGAS/trunk/.... ?? Then you are trying to login on the 'development version'!

I think that you will have to change the URL to http://bioinformatics.psb.ugent.be/webtools/bogas/

OK, thanks !...

But I can't do much with your Bogas display .. sorry ! I need to see SEVERAL genes next to each other and the exon frames and the sequence nucleotide .. in other words, I need an Artemis(-like) interface. I again can't see how to get it when you have accessed a gene in Bogas ! Is there no way to get the annotated model of the whole contig ??

Besides, I tried to get access to the automatic Blast results : I can get the multiple alignment (nice!) but not to the proteins entries in this alignment to understand wheere they come from (several are apparently partial sequences..)

Pierre

P.

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then it should work!

grtz, lieven

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Hi Lieven,

I finally begun looking at Stefan Rensing "annotation" ... or at least at what I can see of it from your mails .. I can't indeed access Bogas properly !

Here below is the message I get when searching for a locus (typing one of the problematic ones of Stefan from the Excel table tyou sent me a while ago..). I get the very same message when trying to access "annotation" ... I don't know if you can explain what's wrong and help me by mail. Otherwise we will have to wait until in the lab, next tuesday.

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/DB/Rails.pm line 128. continue As far as I can judge from the Excel table, there is indeed a big problem with Stefan Rensing """annotation"" : first, it seems that Stefan is simply taking the gene models as they are, and Blast (or whatever else) them against some database of its own. This in itself is a problem : I have nothing against automatic pipelines, but they have to do more than that! Especially in the case of Ectocarpus where doing our very best we know that gene models can be wrong once in a while with fusion or split, even an automatic pipeline shall be made in such a way to point to likely wrong models in one way or another. Second to "annotate" a gene product, homology with a domain or a signature or a partial homology is not enough! One/a pipeline should look for completeness of the product by e.g. looking for the existence of all expected modules, or similarity with close enough homologs allover the sequence (except termini, and allowing gaps), and at least with adequate sequence length and at least return a warning if it not the case. I don't know what this database is made of, but I am pretty concerned in seeing an annotation like "sigma54" ... when we are annotating a eukaryotic organism !! (sigma factors are indeed prokaryotic transcription factors..).

So I will nevertheless look in detail at a few examples of Stefan annotation, as soon as I can access Bogas properly, and write then a draft mail that I would like both Mark & Yves to agree upon to be sent to Stefan.

best,

Pierre -- """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Pierre ROUZE Laboratoire Associe de l'INRA [France] BioInformatics Team Leader Department of Plant Systems Biology Ghent University, Technologie park 927, B-9052 GENT BELGIUM Flanders Interuniversity Institute for Biotechnology VIB Tel:32.933 13694 Cell.Phone: 32.476 638 304 Fax:32.933 13809 pierre.rouze@psb.ugent.be http://www.psb.ugent.be/bioinformatics ___________________________________________________________________

-- """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Pierre ROUZE Laboratoire Associe de l'INRA [France] BioInformatics Team Leader Department of Plant Systems Biology Ghent University, Technologie park 927, B-9052 GENT BELGIUM Flanders Interuniversity Institute for Biotechnology VIB Tel:32.933 13694 Cell.Phone: 32.476 638 304 Fax:32.933 13809 pierre.rouze@psb.ugent.be http://www.psb.ugent.be/bioinformatics

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-- """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Pierre ROUZE Laboratoire Associe de l'INRA [France] BioInformatics Team Leader Department of Plant Systems Biology Ghent University, Technologie park 927, B-9052 GENT BELGIUM Flanders Interuniversity Institute for Biotechnology VIB Tel:32.933 13694 Cell.Phone: 32.476 638 304 Fax:32.933 13809 pierre.rouze@psb.ugent.be http://www.psb.ugent.be/bioinformatics ___________________________________________________________________ -- ============================================================== 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@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 ==============================================================