bp_mask_by_searchp - Online in the Cloud

PROGRAM:

NAME

bp_mask_by_search - mask sequence(s) based on its alignment results

SYNOPSIS

bp_mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa

DESCRIPTION

Mask sequence based on significant alignments of another sequence. You need to provide
the report file and the entire sequence data which you want to mask. By default this will
assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming
you've provided the sequence file for the hit database. If you would like to do the
reverse and mask the query sequence specify the -t/--type query flag.

This is going to read in the whole sequence file into memory so for large genomes this may
fall over. I'm using DB_File to prevent keeping everything in memory, one solution is to
split the genome into pieces (BEFORE you run the DB search though, you want to use the
exact file you BLASTed with as input to this program).

Below the double dash (--) options are of the form --format=fasta or --format fasta or you
can just say -f fasta

By -f/--format I mean either are acceptable options. The =s or =n or =c specify these
arguments expect a 'string'

Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information

AUTHOR - Jason Stajich

Jason Stajich, jason-at-bioperl-dot-org.

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