WWW-BLAST tutorial for Blast2GO

A quick and esay tutorial to set up a local www-BLAST server for Blast2GO under Linux Kubuntu or Ubuntu in 10 easy steps:

1. Download www-BLAST form NCBI $> wget ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/wwwblast-2.2.18-ia32-… (take care about 32 or 64 bits depending on your hardware) 
    
2. Install an Apache Web Server (works automatically in ((k)ubuntu) $> sudo apt-get install apache2 
    
3. Install a csh shell (needed by the Blast Programm, automatically) $> sudo apt-get install csh 
    
4. Copy the unzipped blast folder in /usr/lib/cgi-bin/ and adjust permissions: $> tar xzvf wwwblast-2.2.18-ia32-linux.tar.gz $> cp -R wwwblast-2.2.18-ia32-linux.tar.gz /usr/lib/cgi-bin $> chmod -R 755 /usr/lib/cgi-bin/blast 
    
5. Copy your sequence database (e.g. your_new_db) to the blast DB directory (/usr/lib/cgi-bin/blast/db) (Note that this DB has to be created previously from a fasta file making use of the “formatdb” command) $> cp -R your_new_db.* /usr/lib/cgi-bin/blast/db 
    
6. Add your database to the www-blast configuration file in (/usr/lib/cgi-bin/blast/blast.rc). Behind the algorithm (blastp, blastx) you want to use put your database name (without extensions) seperated by a white space e.g. blastx test_aa_db your_new_db 
    
7. Add you database and the www-blast path to the B2G properties file (/home/your_user_name/blast2go/blast2go.properties) Blast.blastdbs=nr,swissprot,your_new_db Blast.urls=http://localhost/cgi-bin/blast/blast.cgi (seperated from others by a white space) 
    
8. Try the blast server (html and cgi) in a web-browser Put http://localhost/cgi-bin/blast/blast.html (a html page is shown to different types of blasts) 
    
9. Put http://localhost/cgi-bin/blast/blast.cgi?CMD=Put (and error should be returned like “Error 6 in submitting BLAST query” which means that the cgi works fine! ) 
    
10. Try the local Blast installation with Blast2GO setting the corresponding parameters in the Blast dialog. choose the Blast Server URL: http://localhost/cgi-bin/blast/blast.cgi choose the Blast DB: your_new_db choose the correct Blast Program. choose the right Blast Mode: WWW-Blast and press PLAY

Good luck! (author: Stefan Götz)

PD: Another tutorial on how to set up a www-blast server can be found here: http://blog.pansapiens.com/2008/08/25/setting-up-wwwblast-on-ubuntu-apache/