From aperezp at uma.es Thu May 18 06:14:17 2006 From: aperezp at uma.es (=?ISO-8859-1?Q?=22Antonio_J=2E_P=E9rez=22?=) Date: Thu, 18 May 2006 12:14:17 +0200 Subject: [DAS] Protein annotation Message-ID: <446C48F9.2020607@uma.es> Hello everybody, I am a biologist from Spain new in DAS. We would like to build a DAS client, obtaining annotation for protein sequences. We are interesting on general annotation (no positional one) as keywords, GO terms, pubmed abstracts, etc. I have been searching for this information on several reference and annotation servers but I did not find anything. Please, do you know if it exists and where should I search? Regards and thanks, Antonio. -- Antonio J. P?rez Pulido, PhD Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Facultad de Ciencias (Dpto. de Gen?tica) Campus Universitario de Teatinos 29071 M?laga (Spain) http://www.ajperez.cjb.net / antoniojperez at uma.es Tfno. +34 952 131 957 -------------------------------------------------------- Try the server for protein function assigment (AnaGram): http://jaguar.genetica.uma.es/anagram.htm -------------------------------------------------------- From pall at cbs.dtu.dk Thu May 18 06:39:18 2006 From: pall at cbs.dtu.dk (Pall Isolfur Olason) Date: Thu, 18 May 2006 12:39:18 +0200 Subject: [DAS] Protein annotation In-Reply-To: <446C48F9.2020607@uma.es> References: <446C48F9.2020607@uma.es> Message-ID: <446C4ED6.3070706@cbs.dtu.dk> Hey Antonio, The DAS registry at the Sanger center is probably a good place to start looking... There are various servers there for several coordinate systems. http://das.sanger.ac.uk/registry/listServices.jsp with best, Pall Antonio J. P?rez wrote: > Hello everybody, I am a biologist from Spain new in DAS. We would >like to build a DAS client, obtaining annotation for protein sequences. >We are interesting on general annotation (no positional one) as >keywords, GO terms, pubmed abstracts, etc. I have been searching for >this information on several reference and annotation servers but I did >not find anything. > > Please, do you know if it exists and where should I search? > > Regards and thanks, > > Antonio. > > > -- ---------------------------------------------------------------------- Pall Isolfur Olason, PhD student Phone: (+45) 45 25 24 71 Center For Biological Sequence Analysis Fax: (+45) 45 93 15 85 Technical University of Denmark E-mail: pall at cbs.dtu.dk Building 208, Kemitorvet 2800 Lyngby, Denmark ---------------------------------------------------------------------- From aperezp at uma.es Thu May 18 07:17:11 2006 From: aperezp at uma.es (=?ISO-8859-1?Q?=22Antonio_J=2E_P=E9rez=22?=) Date: Thu, 18 May 2006 13:17:11 +0200 Subject: [DAS] Protein annotation In-Reply-To: <446C4ED6.3070706@cbs.dtu.dk> References: <446C48F9.2020607@uma.es> <446C4ED6.3070706@cbs.dtu.dk> Message-ID: <446C57B7.3040703@uma.es> Thank you Pall, we have already looked on Sanger, UniProt, and EnsEMBL servers, but I didn't find keywords, pubmed abstracts or GO terms. I seems be not-implemented yet. Salu2 and thanks again, ANtonio. Pall Isolfur Olason escribi?: > Hey Antonio, > > The DAS registry at the Sanger center is probably a good place to > start looking... > There are various servers there for several coordinate systems. > > > http://das.sanger.ac.uk/registry/listServices.jsp > > > > with best, > Pall > > > > Antonio J. P?rez wrote: > >> Hello everybody, I am a biologist from Spain new in DAS. We would >> like to build a DAS client, obtaining annotation for protein >> sequences. We are interesting on general annotation (no positional >> one) as keywords, GO terms, pubmed abstracts, etc. I have been >> searching for this information on several reference and annotation >> servers but I did not find anything. >> >> Please, do you know if it exists and where should I search? >> >> Regards and thanks, >> >> Antonio. >> >> >> > > -- Antonio J. P?rez Pulido, PhD Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Facultad de Ciencias (Dpto. de Gen?tica) Campus Universitario de Teatinos 29071 M?laga (Spain) http://www.ajperez.cjb.net / antoniojperez at uma.es Tfno. +34 952 131 957 -------------------------------------------------------- Try the server for protein function assigment (AnaGram): http://jaguar.genetica.uma.es/anagram.htm -------------------------------------------------------- From darin.london at duke.edu Mon May 22 11:29:45 2006 From: darin.london at duke.edu (Darin London) Date: Mon, 22 May 2006 11:29:45 -0400 Subject: [DAS] BOSC 2006 2nd Call for Papers In-Reply-To: <4471CE49.80109@duke.edu> References: <44294B65.4050207@duke.edu> <4471CE49.80109@duke.edu> Message-ID: <4471D8E9.8090109@duke.edu> 2nd CALL FOR SPEAKERS This is the second and last official call for speakers to submit their abstracts to speak at BOSC 2006 in Fortaleza, Brasil. In order to be considered as a potential speaker, an abstract must be recieved by Monday, June 5th, 2006. We look forward to a great conference this year. Please consult The Official BOSC 2006 Website at: http://www.open-bio.org/wiki/BOSC_2006 for more details and information. In addition, a BOSC weblog has been setup to make it easier to desiminate all BOSC related announcements: http://wiki.open-bio.org/boscblog/ And if you have an ICAL compatible Calendar, there is an EventDB calendar set up with all BOSC related deadlines. http://eventful.com/groups/G0-001-000014747-0 More information about ISMB can be found at the Official ISMB 2006 Website: http://ismb2006.cbi.cnptia.embrapa.br/ Thank You, and we look forward to seeing you all, The BOSC Organizing Committee. From sachgirl2k4 at gmail.com Mon May 29 01:55:49 2006 From: sachgirl2k4 at gmail.com (namita barnwal) Date: Sun, 28 May 2006 22:55:49 -0700 Subject: [DAS] sifference between various biological databases Message-ID: hi all i wanna get some info about the differences and similarity between various biological database .i.e. structural ,sequence,metabolic pathway,protein interaction,gene expressionetc.if anyone has this info then plz rpy me .i m new to this list From aperezp at uma.es Mon May 29 07:07:55 2006 From: aperezp at uma.es (=?ISO-8859-1?Q?=22Antonio_J=2E_P=E9rez=22?=) Date: Mon, 29 May 2006 13:07:55 +0200 Subject: [DAS] sifference between various biological databases In-Reply-To: References: Message-ID: <447AD60B.30903@uma.es> I am interesting in this kind of annotations too. There is a KEGG DAS server for pathways, but you can not do queries by gene identifiers. Structural information (CATH) is also available from UniProt DAS server. But I am not able to find UniProt keywords or GO terms, for example. Salu2, Antonio. namita barnwal escribi?: > hi all > i wanna get some info about the differences and similarity between > various biological database .i.e. structural ,sequence,metabolic > pathway,protein interaction,gene expressionetc.if anyone has this info then > plz rpy me .i m new to this list > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > > . > > -- Antonio J. P?rez Pulido, PhD Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Facultad de Ciencias (Dpto. de Gen?tica) Campus Universitario de Teatinos 29071 M?laga (Spain) http://www.ajperez.cjb.net / antoniojperez at uma.es Tfno. +34 952 131 957 -------------------------------------------------------- Try the server for protein function assigment (AnaGram): http://jaguar.genetica.uma.es/anagram.htm -------------------------------------------------------- From maxgarcia at ac.uma.es Thu May 25 03:20:52 2006 From: maxgarcia at ac.uma.es (Max) Date: Thu, 25 May 2006 09:20:52 +0200 Subject: [DAS] Server DAS questions Message-ID: <44755AD4.2000908@ac.uma.es> Dear sir, Our projects group is working in the development of a DAS system for annotations of YEAST genes. We are looking for information about DAS servers, in particular we need get pathways by genes, but in other DAS servers like KEGG we cannot recover this information without entry points. Is there any possibility to get it without entry points? Thank you in advance kind regards, Max -- Maximiliano Garc?a Oliver Ing. T?c. en Inform?tica de Sistemas Departamento Arquitectura Computadores. Universidad de M?laga. mailto:maxgarcia at ac.uma.es ------------------------------------------------------------------------ "I've seen things you people wouldn't believe. Attack ships on fire off the shoulder of Orion. I watched C-beams glitter in the dark near the Tannhauser Gate. All those moments will be lost ... in time, like tears in rain ... time to die." Do Androids Dream Of Electric Sheep? <> Philip K. Dick --