BeSTGRID BLAST Server

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Standalone BeSTGRID BLAST Server is built on a virtual machine of the Pleyads Xen Server using CentOS 5.0. BLAST Server could be reached by link WWW BLAST Server.

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.

Retrieved from "http://wiki.test.bestgrid.org/index.php/BeSTGRID_BLAST_Server"