Blast On Gscope Project

Blast Database of a Gscope Project

How to create it

Each Gscope Project has a directory RepertoireDuGenome/banques where you can find the blast databases concerning the project.

The owner of the project can create as many blast database as he wants.

How to create a blast database (for example all proteins)

 cd $RepertoireDuGenome/prottfa
 cat * > $RepertoireDuGenome/banques/AllProttfa
 cd $RepertoireDuGenome/banques
 formatdb -i AllProttfa -p T

this can be done by

 gscope CreeUneBanqueBlast AllProttfa

Attention ! if somebody uses Wscope (Gscope on the Web) the first available database will be choosen as default database, so the alphabetic order is important (anyway, the user can check what he wants ...)

How to use it

 blastall -p blasp -i YourInputFasta.tfa -o YourOutputFile.blast -d $RepertoireDuGenome/banques/AllProttfa

and ... on the web, the fommular appears when you do a search.

 http://www-bio3d-igbmc.u-strasbg.fr/~ripp/cgi-bin/gscope_html_server.tcsh?ProGS&RechercheMoi

Database not available

If you are on the web and no database appears, please ask the owner of the database to create it, or mail to Raymond.