RE-PCR(1)
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
SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt
bioperl(1), e-pcr(1), 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.