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Scripts for automating blasts

Pierre Rioux riouxp at IRO.UMontreal.CA
Thu Jun 20 12:17:20 EST 1996

Gordon MacPherson (gordonm at Adenine.Neither_Here.Nor.There) wrote:
:  Does anyone have any scripts which automate blast searches with large
: numbers of sequence files?

: Thanks.

    You can try the "bblast" perl script, available at


    A sample bblast session looks like this:

unix% bblast

    bblast 3.0 Copyright (C) 1995 OGMP     
  Organelle Genome Megasequencing Program  
   This program is distributed under the   
DISTRIBUTION and COPYING that came with it.

Input filename? (enter a "-" to summon a text editor) [prot.lst] prot_in_fasta
Your input file looks like it contains protein sequences.
Type of sequence: (d)na or (p)rotein? [protein] p
Minimum acceptable sequence length? [48] 30
Method of query: (e)mail, (n)etwork or (l)ocal? [network] n
Compare your sequences to what type of database (dna/protein): [protein] p
Do you also want to receive the report(s) by mail? [n] n
Protein Databases: nr, pdb, spdb, kabat, alu, swissprot, month.
Database to use: [nr] nr
Output directory? [/users/riouxp] 


    It can also be used fully automatically, in batch mode, by supplying
all the information with command-line arguments.


 | riouxp at iro.umontreal.ca | Un chat éponge avec son corps un petit     |
 | riouxp at bch.umontreal.ca | morceau de plancher que le soleil éclaire. |

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