November 2007 - beg-bogas@psb.ugent.be

[Beg-bogas] (no subject)
by Patrice Lerouge 14 Nov '07

14 Nov '07

Dear colleague, Mark Cock from Roscoff told me to contact you in order to get a password for access to the Ertocarpus genome data. Sincerely yours, Patrice LEROUGE

1 0

[Beg-bogas] iemand slaagt erin om lege structures te posten
by Lieven Sterck 14 Nov '07

14 Nov '07

URGENT!!!! L.

2 1

[Beg-bogas] [Fwd: Re: [Fwd: Re: Ectocarpus proteins]]
by Lieven Sterck 14 Nov '07

14 Nov '07

ik peis dat het prob is dat de structure 2x gesaved wordt!!! als ge save drukt in artemini wordt de nieuwe strucuture gesaved, maar dan zitte op de edit page en als ge daar uit wilt geraken wilt geraken moet ge submit record duwen => weer ne save en dan het prob... : dat is dan den ouwe struct die gesaved wordt (nl oude die op de edit page stond!!) artemini terug naar index ipv edit zou oplossing zijn denk ik? maar of dat best is?? L. ---------------------------- Original Message ---------------------------- Subject: Re: [Fwd: Re: Ectocarpus proteins] From: melias(a)natur.cuni.cz Date: Tue, November 13, 2007 11:15 am To: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> -------------------------------------------------------------------------- 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 >>>>> 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 >>>>> ============================================================== >> >> > > > > > > > > >

2 1

[Beg-bogas] ah man!!!
by Lieven Sterck 14 Nov '07

14 Nov '07

nu ister blijkbaar geen prot alster ne struct gemodified is!! waarschijnlijk omdat er voor dienen date (van de struc edit) geen prot entry is.... oplossing?? *moeten echt da date gedoe uit 'sorten' *alster struc edit is, ook prot entry maken!! in upload_embl.pl L.

1 0

[Beg-bogas] Ectocarpus Genome Annotation
by Carl Carrano 12 Nov '07

12 Nov '07

According to directions received from Mark Cock I am requesting to create a login account for this project. Regards C.J. Carrano ________________________________ Carl J. Carrano, Professor and Chair Department of Chemistry San Diego State University San Diego, CA 92182-1030 phone 619-594-5929 fax: 619-594-4634 email: carrano(a)sciences.sdsu.edu ________________________________

2 1

[Beg-bogas] Re: BOGAS
by maumus＠biologie.ens.fr 12 Nov '07

12 Nov '07

Hi, I think there is no valid link in there. > Hi, you have been invited to take part in the annotation of Ectoca= > rpus. Please click on following link to activate your > user account: <a > href=3D'http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitatio= > ncode/ea2d0f22dfc8e7d5fcbbf565e0106e4a'>ea2d0f22dfc8e7d5fcb > bf565e0106e4a</a> If the link doesn't work, try to go to http://bi= > oinformatics.psb.ugent.be/webtools/bogas/users/enteric > and enter ea2d0f22dfc8e7d5fcbbf565e0106e4a with kind regards, t= > he BOGAS team >

1 0

[Beg-bogas] request for register and log in
by Taizo Motomura 12 Nov '07

12 Nov '07

Dear sir, I am Taizo Motmura, Hokkaido University, a member of Ectocarpus genome annotation project. Would you teach me "User name" and "Password" for BOGAS. Thank you. Best wishes, Taizo Motomura ======================================== Taizo Motomura Muroran Marine Station Field Science Center for Northern Biosphere Hokkaido University Muroran 051-0003, Hokkaido, Japan TEL: +81 143 22 2846 FAX: +81 143 22 4135 e-mail: motomura(a)bio.sci.hokudai.ac.jp ========================================

1 0

[Beg-bogas] [Fwd: Re: Ectocarpus proteins]
by Lieven Sterck 11 Nov '07

11 Nov '07

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 >>>> VÃ©gÃ©taux Marins et BiomolÃ©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] Artemini 2.10
by Thomas Abeel 09 Nov '07

09 Nov '07

I have uploaded Artemini 2.10 Improvements: - When the program starts it will center on the CDS sequence if present - Mail addresses on errors are all beg-bogas - Program has a bit more error reporting - Fixed bug where upper case amino acid sequences could not be found. - The name displayed is nicely formatted on the title bar - Artemini now takes into account the offset if it is present in the source EMBL file. greetings, Thomas

1 0

[Beg-bogas] mighty administrator
by Yao-Cheng Lin 09 Nov '07

09 Nov '07

Dear mighty system administrator, Could you please give me an account to access the BOGAS? Best, Yao-Cheng

1 0