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root/yamap/big_blast.txt
Revision: 1.1
Committed: Mon Sep 11 13:36:01 2006 UTC (10 years, 2 months ago) by knirirr
Branch: MAIN
CVS Tags: HEAD
Log Message:
Various fixes, added transterm.

Line File contents
1 usage: /usr/local/bin/big_blast.pl [-l] [-t|-x|-tx] [-S size] [-j num] [-M num] database input_file [blast options]
2 or: /usr/local/bin/big_blast.pl [-M num] blast_output_file
3 or: /usr/local/bin/big_blast.pl -h (for help)
4
5 -l use lsrun to share the blast jobs over multiple machines
6 -x selects blastx instead of blastn
7 -t selects tblastn instead of blastn
8 -tx selects tblastx instead of blastn
9 -j num sets the number of blast jobs to run simultaneously
10 -M num sets the minimum score for the output hits (default 0)
11 -S num sets the maximum size of sequences sent to blast (default 50000)
12 -w use wublast instead of blast1.4
13 -2 use blast2 not blast1.4
14
15 The first form of the command will run blast on the given input_file
16 against the given database. The -S flag sets the size of the pieces of
17 sequence that are passed to blast. All arguments after the input_file
18 parameter will be passed directly to blast.
19
20 The second form reads and processes the given blast_output_file to
21 produce an MSPcrunch crunch file and an EMBL feature table.
22
23 In both cases there are two output files. One is an EMBL feature
24 table with one feature per hit. The other is a file in the
25 format generated by MSPcrunch -d.