BeSTGRID BLAST Server
From BeSTGRID
[edit] Configuration
Standalone BeSTGRID BLAST Server is built on a virtual machine of the Pleyads Xen Server using CentOS 5.0.
Software has been downloaded from NCBI BLAST Web Server and installed according manuals: ReadMe One and ReadMe Two.
A location of the GenBank Database is New Zealand Biomirror. Daily script uncompresses the GenBank database and places it into that folder. Then the database is formatted by formatdb utility:
./formatdb -i rel###.fsa_aa -p T -n fsa_aa_db -o
where
-i rel###.fsa_aa - input file with release number ### -p T - type of file, T for protein -n fsa_aa_db - base name for BLAST files -o - parse SeqID and create indexes
Resulted BLAST files are copied to db/ sub-folder together with rel###.fsa_aa which is renamed to fsa_aa_db. This folder is a NFS share of the BeSTGRID Data Storage and mounted on WWW BLAST Server on a folder /var/www/html/db.
To connect the GenBank database to BLAST several configuration and html files of BLAST installation have been updated:
- blast.rc and psiblast.rc
blastn fsa_aa_db blastp fsa_aa_db blastx fsa_aa_db tblastn fsa_aa_db tblastx fsa_aa_db
- blast.html, blast_cs.html, megablast.html, megablast_cs.html, psiblast.html, psiblast_cs.html
<select name = "DATALIB"> .... <option VALUE = "fsa_aa_db"> fsa_aa_db </select>
Finally a copy of blast.cgi script file has been created with name Blast.cgi. That is a requirements of Geneious plug-in.
All updated html and configuration files are placed in SVN repository.
