NAME

re-PCR — Find sequence tagged sites (STS) in DNA sequences

SYNOPSIS

re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]

re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]

re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]

re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]

DESCRIPTION

Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by performing STS and primer searches.

OPTIONS

-p=hash-file: Perform primer lookup using hash-file
-P=hash-file: Perform primer lookup using hash-file
-s=hash-file: Perform STS lookup using hash-file
-S=hash-file: Perform STS lookup using hash-file
-n=mism: Set max allowed mismatches per primer for lookup
-g=gaps: Set max allowed indels per primer for lookup
-m=margin: Set variability for STS size for lookup
-l: Use presize alignments (only if gaps>0)
-G: Print alignments in comments
-d=min-max: Set default STS size
-r=+|-: Enable/disable reverse STS lookup
-O=+|-: Enable/disable syscall optimisation
-C=batchcnt: Set number of STSes per batch
-o=outfile: Set output file name
-q: Quiet (no progress indicator)

EXAMPLE

famap -tN -b genome.famap org/chr_*.fa

fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

See famap(1) and fahash(1)

AUTHORS

This manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

April 2008