famap1
Prepare fasta sequence database for re-pcr searches
Usage
famap [-hV]
-b
mmapped-file
[-t
cvt]
[fafile ...]
famap [-hV]
-d
mmapped-file
[ord ...]
famap [-hV]
-l
mmapped-file
[ord ...]
Overview
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, |
|
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N - nucleotide uppercase allowed [ACGTN] |
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nx - nucleotide with ambiguity codes allowed |
|
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NX - nucleotide with ambiguity codes uppercase |
Examples
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)
Releases
9 releases since Debian 5.0 (Lenny); the text changed 1 time.