NAME

       fahash - sequence hash builder for reverse e-PCR

SYNOPSIS

       fahash  [-hV] -b hash-file [-w wdsize] [-f period] [-F fragment_min,fragment_max] [-k] [-c
       cachesize] [-v 1|2] famap-file ...

       fahash [-hV] -T hash-file [-o outfile]

DESCRIPTION

       The program fahash is part of the e-PCR suite and is used to build hash-files, and  output
       word usage statistics for reverse e-PCR searches.

OPTIONS

       -b hash-file
              Build hash tables (hash-file) from sequence files,

       -T hash-file
              Print word usage statistics for hash-file

       -o outfile
              Write output to file `outfile'

   build-options:
       -w wordsize
              Set word size when building hash tables

       -f period
              Set discontiguity when building hash tables

       -k     Skip repeats when building hash-file

       -F min,max
              Set watermarks for fragment size (in Mb) (version 1 only)

       -c cachesize
              Set cache size (version 2 only)

       -v ver Use format version (1|2, 2 is default)

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 re-pcr(1)

SEE ALSO

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

       bioperl(1), e-pcr(1), famap(1) and re-pcr(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.

Reverse e-PCR: sequence hash builder versionApril92008                                  FAHASH(1)