Difference between revisions of "Blast On Gscope Project"
| (2 intermediate revisions by the same user not shown) | |||
| Line 2: | Line 2: | ||
==How to create it== | ==How to create it== | ||
| − | Each Gscope Project has a directory '''RepertoireDuGenome/banques''' where you can find the blast databases concerning the project. | + | 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. | The owner of the project can create as many blast database as he wants. | ||
| Line 17: | Line 17: | ||
gscope CreeUneBanqueBlast AllProttfa | 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 ...) | + | 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== | ==How to use it== | ||
| Line 23: | Line 23: | ||
blastall -p blasp -i YourInputFasta.tfa -o YourOutputFile.blast -d $RepertoireDuGenome/banques/AllProttfa | blastall -p blasp -i YourInputFasta.tfa -o YourOutputFile.blast -d $RepertoireDuGenome/banques/AllProttfa | ||
| − | and ... on the web the | + | 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== | ==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. | If you are on the web and no database appears, please ask the owner of the database to create it, or mail to Raymond. | ||
Latest revision as of 11:32, 9 September 2010
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.
