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ncbi-epcr - Tool to test a DNA sequence for the presence of sequence tagged sites…  more info»

fahash.1.gz

FAHASH(1)                   User Commands                  FAHASH(1)



NAME
       fahash - sequence hash builder for reverse e-PCR


SYNOPSIS
       fahash  [-hV]  -b hash-file [-w wdsize] [-f period] [-F frag‐
       ment_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  Pub‐
       lic  License,  Version  2  any later version published by the
       Free Software Foundation.


       On Debian systems, the complete text of the GNU General  Pub‐
       lic License can be found in /usr/share/common-licenses/GPL.



Reverse e-PCR: sequence hash Aprile2008rsion 2.3.9         FAHASH(1)
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