[Bioperl-l] Extraction from UniProt flatfile

[Sean Davis]

Stephen,

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:

http://hgdownload.cse.ucsc.edu/goldenPath/uniProt/database/

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:

host:  genome-mysql.cse.ucsc.edu
User:  genome
password:  There isn't one (leave it blank)

Hope this helps.

Sean

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 
> you
> need. The database schema is in a repository biosql-schema as it is 
> shared
> among several language projects.
>
> 	-Heikki
>
>
>
>> 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,
>>
>>  Stephen
>>
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>
> -- 
> ______ _/      _/_____________________________________________________
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>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
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