fasta and blast searches

Thure Etzold etzold at ebi.ac.uk
Thu Feb 20 11:09:36 EST 1997

Janice Coventry, Walter and Eliza Hall Institute wrote:
> Hello,
> Can anyone help me with blast and fasta searches?  Do the blast and fasta
> sources come with srs or do you have to have the programs running on the
> machine srs is running on?

The SRS release does not contain any of these application programs but the next release
5.03 will support BLAST, FASTA and the Smith and Waterman search with the Bioccelerator.
Also it supports Clustalw for multiple sequence alignment. 

The applications can be started on machines other than the one hosting the SRSWWW server
through rshells. It is also possible to customize and add more search tools. I am 
currently writing documentation on how to do that. The integration with application
programs is still at an exp. stage and the goal is to allow integration of many more

> Also to set up the searches do you just have to uncomment the relevant parts of
> srsdb.i and run srssection?

it will be something like that - but most likely some customization will have to be
done - such as the path to the blast and fasta databanks


> Thanks,
> Janice

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