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standalone_blast [2014/11/21 13:56]
sebastien.renaut
standalone_blast [2014/11/21 14:19]
sebastien.renaut
Line 54: Line 54:
   *gi_viridiplantae contains a list of all GI for all viriplantae. This speeds things up a lot since it restrict the search to plants only.   *gi_viridiplantae contains a list of all GI for all viriplantae. This speeds things up a lot since it restrict the search to plants only.
 <​code>​ <​code>​
-$ blastp -query mygenes.fasta -db ~/​blast/​database/​ncbi_nr/​nr -gilist ​~/​blast/​database/​green_plants/​gi_viridiplantae -outfmt 4 -out mygenes.blast.out+$ blastp -query mygenes.fasta -db ~/​blast/​database/​ncbi_nr/​nr -gilist gi_viridiplantae -outfmt 4 -out mygenes.blast.out
 </​code>​ </​code>​
   *To get a GI list, go to http://​www.ncbi.nlm.nih.gov/​   *To get a GI list, go to http://​www.ncbi.nlm.nih.gov/​