- beg-bogas@psb.ugent.be - maillist.psb.ugent.be

[Beg-bogas] Ectocarpus - Chloroplast genome
by Gildas Le Corguille 16 Jan '08

16 Jan '08

Hello, I'm annotator on the chloroplast genome of Ectocarpus. It's a project beside the nuclear genome. It's seem that some contigs on bogas belong to the chloroplast genome. Then to prevent the double annotation, it may be a good idea to delete those contigs. We can search for then if you don't know exactly which they are. Best regards Gildas Le Corguillé and Catherine Le Blanc

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[Beg-bogas] account for annotation of Ectocarpus
by nyvall＠sb-roscoff.fr 15 Jan '08

15 Jan '08

Hi, I would like to get an account to be able to participate in the annotation of the Ectocarpus siliculosus genome. Yours scincerely, Pi Nyvall ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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[Beg-bogas] [Fwd: Re: Stefan ... & BOGAS (2)]
by lieven sterck 08 Jan '08

08 Jan '08

-------- Original Message -------- Subject: Re: Stefan ... & BOGAS (2) Date: Tue, 08 Jan 2008 09:54:29 +0100 From: Pierre Rouze <pirou(a)psb.UGent.be> To: Lieven Sterck <lieven.sterck(a)psb.ugent.be> References: <477F3B8A.4090704(a)psb.UGent.be> <19271.157.193.202.129.1199536388.squirrel(a)webmail.psb.ugent.be> <477FCB57.8020606(a)psb.UGent.be> <4781EF18.40908(a)psb.ugent.be> <47826356.9050303(a)psb.UGent.be> <51222.157.193.202.129.1199747946.squirrel(a)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 > > > >> lieven sterck wrote: >> >>> 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. >> >>> grtz, >>> lieven >>> >>> Pierre Rouze wrote: >>> >>>> Lieven Sterck wrote: >>>> >>>>> 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. >>>> >>>>> then it should work! >>>>> >>>>> grtz, >>>>> lieven >>>>> >>>>> >>>>> >>>>>> 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(a)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(a)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(a)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(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] login/password request
by Bernard Billoud 07 Jan '08

07 Jan '08

Dear administrator, Having attended the initiation session at Evry, I thought I had a login/password for the BOGAS site... which I could not remember. I submitted a request on the "Forgot password" page of the website, but did not receive any answer yet. Maybe my username is neither billoud nor bernard.billoud (but I cannot figure out what other login I may have chosen). Would you please give my login/password if I already have them, or to create a new identifier for me ? Thanks in advance Sincerly, Bernard Billoud -- Bernard Billoud - Atelier de BioInformatique | You've got the answer | Bâtiment de la Pédagogie, Aile C, RdC, Pièce 4 | in your hand ? | BC1202 - UPMC - 4 place Jussieu - F75005 Paris | Throw it away. | Tel. (1) 44 27 65 51 ~~ Fax. (1) 44 27 63 12 | (Joe Jackson) |

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[Beg-bogas] Ectocarpus annotation: creation of an account
by charrier＠sb-roscoff.fr 03 Jan '08

03 Jan '08

Dear 'you' (Lieven?), I'd be very grateful to you if I could get a username and a password to allow me to start bringing my contribution to the annotation of the Ectocarpus genome (on the bogas interface). Thanks also for your new year's best wishing. Same to you. Thanks in advance; Bénédicte Charrier ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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[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 >>> ============================================================== >> >> > >

1 0

[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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