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

       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)

       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.

        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)

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

-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)

       /usr/share/doc/ncbi-epcr/README.txt

       bioperl(1), e-pcr(1), famap(1) and fahash(1)

re-PCR[-hV]-phash-file[-ggaps][-nmism][-lq][primer...]re-PCR[-hV]-Phash-file[-ggaps][-nmism][-l][-mmargin][-O+|-][-Cbatchcnt][-ooutfile][-r+|-][primers-file...]re-PCR[-hV]-shash-file[-ggaps][-nmism][-lq][-mmargin][-ooutfile][-r+|-][leftrightlo[-hi][...]]re-PCR[-hV]-Shash-file[-ggaps][-nmism][-lq][-mmargin][-O+|-][-Cbatchcnt][-ooutfile][-r+|-][stsfile...]