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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

    ftp://megasun.bch.umontreal.ca/pub/bblast

    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   
 GNU GENERAL PUBLIC LICENSE. See the files 
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] 

etc.

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

    Pierre



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