1BP_MASK_BY_SEARCH(1)  User Contributed Perl Documentation BP_MASK_BY_SEARCH(1)
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NAME

6       mask_by_search - mask sequence(s) based on its alignment results
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SYNOPSIS

9         mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
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DESCRIPTION

12       Mask sequence based on significant alignments of another sequence.  You
13       need to provide the report file and the entire sequence data which you
14       want to mask.  By default this will assume you have done a TBLASTN (or
15       TFASTY) and try and mask the hit sequence assuming you've provided the
16       sequence file for the hit database.  If you would like to do the
17       reverse and mask the query sequence specify the -t/--type query flag.
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19       This is going to read in the whole sequence file into memory so for
20       large genomes this may fall over.  I'm using DB_File to prevent keeping
21       everything in memory, one solution is to split the genome into pieces
22       (BEFORE you run the DB search though, you want to use the exact file
23       you BLASTed with as input to this program).
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25       Below the double dash (--) options are of the form --format=fasta or
26       --format fasta or you can just say -f fasta
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28       By -f/--format I mean either are acceptable options.  The =s or =n or
29       =c specify these arguments expect a 'string'
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31       Options:
32           -f/--format=s    Search report format (fasta,blast,axt,hmmer,etc)
33           -sf/--sformat=s  Sequence format (fasta,genbank,embl,swissprot)
34           --hardmask       (booelean) Hard mask the sequence
35                            with the maskchar [default is lowercase mask]
36           --maskchar=c     Character to mask with [default is N], change
37                            to 'X' for protein sequences
38           -e/--evalue=n    Evalue cutoff for HSPs and Hits, only
39                            mask sequence if alignment has specified evalue
40                            or better
41           -o/--out/
42           --outfile=file   Output file to save the masked sequence to.
43           -t/--type=s      Alignment seq type you want to mask, the
44                            'hit' or the 'query' sequence. [default is 'hit']
45           --minlen=n       Minimum length of an HSP for it to be used
46                            in masking [default 0]
47           -h/--help        See this help information
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AUTHOR - Jason Stajich

50       Jason Stajich, jason-at-bioperl-dot-org.
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54perl v5.12.0                      2010-04-29              BP_MASK_BY_SEARCH(1)