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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)
   1. Blast.blastdbs=nr,swissprot,your_new_db
   2. Blast.urls=http://localhost/cgi-bin/blast/blast.cgi
   3. (seperated from others by a white space)
8. Try the blast server (html and cgi) in a web-browser
   1. 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.
    1. choose the Blast Server URL: http://localhost/cgi-bin/blast/blast.cgi
    2. choose the Blast DB: your_new_db
    3. choose the correct Blast Program.
    4. choose the right Blast Mode: WWW-Blast
    5. 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/