re-PCR(1) 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 <[email protected]> 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.