Man pages sections > man1 > famap

famap - prepare Fasta sequence database for re-PCR searches

FASTA(1) User Commands FASTA(1)

NAME

famap - prepare Fasta sequence database for re-PCR searches
 

SYNOPSIS

famap [-hV] -b mmapped-file [-t cvt] [fafile ...]
famap [-hV] -d mmapped-file [ord ...]
famap [-hV] -l mmapped-file [ord ...]
 

DESCRIPTION

The program famap is part of the e-PCR suite and is used to build mmapped-file from FASTA files for reverse e-PCR searches
 

OPTIONS

where cvt (conversion table) is one of:
off - as is (default)
n - nucleotide [acgtnACGTN] allowed,
N - nucleotide uppercase allowed [ACGTN]
nx - nucleotide with ambiguity codes allowed
NX - nucleotide with ambiguity codes uppercase
 
 

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.
April 2008 Fasta converter for e-PCR version 2.3.9