BLAST2COL

Section: User Commands (1)
Updated: September 2000
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NAME

blast2col - convert BLAST output format to col format.

blast2col: [-expect=expect] [-length=length] [-similarity=similarity] [-score=score] [-top=top] [-mismatch=mismatch] [-alignlen=alignlen] [-ignore=ignore] [file]

blast2col converts BLAST output to col format. Input is either from file or stdin. The output is sent to stdout.

blast2col accepts the following options:

--expect=expect: Sets maximum limit for expect value of hits to be converted. expect is a decimal number

--length=length: Sets minimum limit for alignment length of hits to be converted. length is an integer.

--similarity=similarity: Sets minimum limit for matches relative to length of hits to be converted. similarity is an integer from 0 to 1.

--score=score: Sets minimum limit for score value of hits to be converted. score is a decimal number

--mismatch=mismatch: Sets maximum limit for number of mismatches of hits to be converted. mismatch is an integer.

--alignlen=alignlen: Sets minimum limit for alignment length relative to query length of hits to be converted. alignlen is an integer from 0 to 1.

--ignore=ignore: Specifies mismatches that should be ignored. ignore is a string of nucleotide pairs, separated by commas. E.g. `GT,TG' specifies that G-T mismatches (both ways) should be ignored when deciding which sequences to convert.

Convert blast file to col file.

Convert blast file to col file. Only convert hits that has at most 5 mismatches and has a length of at least 40, while 90% of the hit is matches.

--top option does not work.

Report other bugs to col-bugs@bioinf.au.dk.

Bjarne Knudsen (bk@daimi.au.dk)

Comments, questions, etc., email gorodkin@rth.dk.

Last updated March 26th, 2007 by Jan Gorodkin