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@psb.ugent.be>:

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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

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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@psb.ugent.be>:

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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@psb.ugent.be> Date: Thu, November 8, 2007 11:17 pm To: melias@natur.cuni.cz Cc: cock@sb-roscoff.fr beg-bogas@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

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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@psb.ugent.be>:

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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@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@natur.cuni.cz >>> To: Kenny Billiau <kenny.billiau@psb.ugent.be> >>> References: >>> <20071102114032.ry1oc3gmmjcckc8s@www.natur.cuni.cz> >>> <472B0B6C.8060706@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@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@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@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@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 >> ==============================================================