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standalone_blast [2014/11/21 13:55]
sebastien.renaut
standalone_blast [2014/11/21 14:43] (current)
sebastien.renaut
Line 52: Line 52:
 ### BLASTp with gi restriction###​ ### BLASTp with gi restriction###​
   *protein against protein   *protein against protein
-  *gi_viriplantae ​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_viriplantae ​-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/​
-  *Search for "http://​www.ncbi.nlm.nih.gov/​" in "​protein"​ database. +  *Search for "viridiplantae" in "​protein"​ database. 
-  *Download all GI (top right, >send to, >choose destination file,>​format ​gi list,>create file)+  *Download all GI (top right, >send to, >choose destination file, >​format ​gilist, >create file)
  
-===== Sequence searches using standalone BLAST =====+===== More examples ​===== 
 +###Sequence searches using standalone BLAST
 In January 2011, Annie Archambault (research professional at the [[http://​qcbs.ca/​|QCBS]]) and [[http://​www.bio.umontreal.ca/​personnel/​CAMERON_Christopher/​index.html|Christopher Cameron]] (professor at Université de Montréal) set up a sequence similarity between 451 spicule matrix proteins from the sea urchin (Strongylocentrotus purpuratus, an echinoderm) that are involved in biomineralization ((Mann K, Wilt FH, Poustka AJ (2010) Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix. Proteome Science 8 DOI 33 10.1186/​1477-5956-8-33)) and the genome of //​Saccoglossus kowlevskii//​ (a hemichordate that forms biominerals) and //Ciona// (a hemichordate that do not form biominerals).  ​ In January 2011, Annie Archambault (research professional at the [[http://​qcbs.ca/​|QCBS]]) and [[http://​www.bio.umontreal.ca/​personnel/​CAMERON_Christopher/​index.html|Christopher Cameron]] (professor at Université de Montréal) set up a sequence similarity between 451 spicule matrix proteins from the sea urchin (Strongylocentrotus purpuratus, an echinoderm) that are involved in biomineralization ((Mann K, Wilt FH, Poustka AJ (2010) Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix. Proteome Science 8 DOI 33 10.1186/​1477-5956-8-33)) and the genome of //​Saccoglossus kowlevskii//​ (a hemichordate that forms biominerals) and //Ciona// (a hemichordate that do not form biominerals).  ​