Heb aangepast dat hij nu 2 genen up en down geeft (ipv 1 vroeger). lieven Thomas Abeel wrote:
De oorzaak is dat de nieuwe coordinate die hij opgeeft buiten de sequentie in de gepadde Ns vallen. Waardoor dat in eerste instantie lijkt te lukken, maar dan gaat Artemini de mist in bij het saven omdat hij probeert die coordinaten aan te passen, wat niet gaat omdat die negatief worden.
De enige mogelijkheid die ik hier zie is om meer sequentie door te geven zodat Artemini niet zoveel moet padden.
Ofwel EMBL formaat uitbreiden zodat die ook negatieve coordinaten aankan. Maar hoe dan ook lijkt me dat nogal veel werk.
Mij lijkt het eerste (meer/alle sequentie) het eenvoudigste.
T
Lieven Sterck schreef:
no problemo!! gheb tan ook conge, wa ;-)
tkan trouwens ook in de perl zitten ...
L.
Dat zal voor morgen zijn zenne.
T
Lieven Sterck schreef:
Hi Marek,
sorry for that! We'll look into it.
thanks, lieven
Hi Lieven,
I am working hard on the annotation but unfortunatelly still some unexpected problems emerge. Now I face a trouble with annotating the gene Esi0030_0124. When I insert the correct coordinates, which are as follows:
570185..570280,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975
However, after I try to save the change to the server, the program replies with an error message, and when I open the window with the coordinates, they are changed so that they look like this:
2,574970..575068,575392..575581,576259..576353,577128..577181,579928..579975
I have not seen this behaviour with other genes, so I have no explanation for it. What is going on?
Thanks, Marek
Cituji Lieven Sterck <lieven.sterck@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@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 >>>>>>>> ============================================================== >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>
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-- ============================================================== 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 ==============================================================