fahash − sequence hash builder for reverse e-PCR
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]
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.
−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) |
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
/usr/share/doc/ncbi-epcr/README.txt
bioperl(1), e-pcr(1), famap(1) and re-pcr(1)
This manual page was written by Andreas Tille <tille AT debian DOT 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.