http://lbgi.igbmc.fr/wikili/index.php?title=Special:Recentchanges&feed=atom 2010-09-08T04:24:48Z Track the most recent changes to the wiki in this feed. MediaWiki 1.12.0 http://lbgi.igbmc.fr/wikili/index.php?title=Blast_On_Gscope_Project&diff=2761&oldid=prev 2010-09-06T15:36:13Z

<p></p> <p><b>New page</b></p><div>Blast Database of a Gscope Project<br /> <br /> ==How to create it==<br /> Each [[Gscope]] Project has a directory '''RepertoireDuGenome/banques''' where you can find the blast databases concerning the project. <br /> <br /> The owner of the project can create as many blast database as he wants.<br /> <br /> How to create a blast database (for example all proteins)<br /> <br /> cd $RepertoireDuGenome/prottfa<br /> cat * &gt; $RepertoireDuGenome/banques/AllProttfa<br /> cd $RepertoireDuGenome/banques<br /> formatdb -i AllProttfa -p T<br /> <br /> this can be done by <br /> <br /> gscope CreeUneBanqueBlast AllProttfa<br /> <br /> 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 ...)<br /> <br /> ==How to use it==<br /> <br /> blastall -p blasp -i YourInputFasta.tfa -o YourOutputFile.blast -d $RepertoireDuGenome/banques/AllProttfa<br /> <br /> and ... on the web, the fommular appears whern you do a search.<br /> <br /> http://www-bio3d-igbmc.u-strasbg.fr/~ripp/cgi-bin/gscope_html_server.tcsh?ProGS&amp;RechercheMoi<br /> <br /> ==Database not available==<br /> <br /> If you are on the web and no database appears, please ask the owner of the database to create it, or mail to Raymond.</div>

Ripp