[Bioperl-l] Extraction from UniProt flatfile
sdavis2 at mail.nih.gov
Tue Mar 8 05:57:38 EST 2005
There is another alternative that may meet your needs. The folks at
the UCSC genome browser maintain a relationalized version of uniprot
(i.e., a MySQL database) here:
that is available for download.
You can connect directly to it (for SQL queries) via their genome mysql
server (open to the public). Connection information is:
password: There isn't one (leave it blank)
Hope this helps.
On Mar 8, 2005, at 4:11 AM, Heikki Lehvaslaiho wrote:
> Take a look at the BioSQL project. There is a cvs repository called
> bioperl-db. It contains the script load_seqdatabase.pl, that does what
> need. The database schema is in a repository biosql-schema as it is
> among several language projects.
>> I am writing a perl program that will extract data from a UniProt
>> flatfile so that I can automatically put data into
>> my PostgreSQL database. I am taking out name, protein ID number,
>> references etc from the file.
>> Does anyone know if there is a script available to do this already?
>> Many thanks,
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
> ______ _/ _/_____________________________________________________
> _/ _/ http://www.ebi.ac.uk/mutations/
> _/ _/ _/ Heikki Lehvaslaiho heikki at_ebi _ac _uk
> _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
> _/ _/ _/ Wellcome Trust Genome Campus, Hinxton
> _/ _/ _/ Cambridge, CB10 1SD, United Kingdom
> _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
More information about the Bioperl-l