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@natur.cuni.cz To: Lieven Sterck <lieven.sterck@psb.ugent.be> References: <58246.157.193.202.129.1194749039.squirrel@webmail.psb.ugent.be> <20071113111523.7qanxvnt3t4zggcg@www.natur.cuni.cz> <35316.157.193.202.129.1194998042.squirrel@webmail.psb.ugent.be> <20071114191407.oj2lemhpebegw00s@www.natur.cuni.cz> <44719.157.193.202.129.1195088065.squirrel@webmail.psb.ugent.be> <20071115162254.65qzjhw4ihw04s0g@www.natur.cuni.cz> <53689.157.193.202.129.1195164829.squirrel@webmail.psb.ugent.be> <20071116221047.oekxk8bj8668wgk4@www.natur.cuni.cz> <15272.157.193.202.129.1195254098.squirrel@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@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

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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@psb.ugent.be>:

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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

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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@psb.ugent.be>:

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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

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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>:

> 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@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@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 >>> >>> >>>> 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>: >>>> >>>>> 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 >>>>>>> ============================================================== >>>> >>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> > >

-- ============================================================== 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 ==============================================================