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)

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.

                                            April 2008                                  RE-PCR(1)