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.