re-PCR1
Find sequence tagged sites (sts) in dna sequences
Usage
re-PCR [-hV]
-p
hash-file
[-g
gaps]
[-n
mism]
[-lq]
[primer ...]
re-PCR [-hV]
-P
hash-file
[-g
gaps]
[-n
mism]
[-l]
[-m
margin]
[{-O+ | -}]
[-C
batchcnt]
[-o
outfile]
[{-r+ | -}]
[primers-file ...]
re-PCR [-hV]
-s
hash-file
[-g
gaps]
[-n
mism]
[-lq]
[-m
margin]
[-o
outfile]
[{-r+ | -}]
[left
right
lo
[-hi]
[]]
re-PCR [-hV]
-S
hash-file
[-g
gaps]
[-n
mism]
[-lq]
[-m
margin]
[{-O+ | -}]
[-C
batchcnt]
[-o
outfile]
[{-r+ | -}]
[stsfile ...]
Overview
Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by performing STS and primer searches.
Options
-
-p=hash-file -
Perform primer lookup using hash-file
-
-P=hash-file -
Perform primer lookup using hash-file
-
-s=hash-file -
Perform STS lookup using hash-file
-
-S=hash-file -
Perform STS lookup using hash-file
-
-n=mism -
Set max allowed mismatches per primer for lookup
-
-g=gaps -
Set max allowed indels per primer for lookup
-
-m=margin -
Set variability for STS size for lookup
-
-l -
Use presize alignments (only if gaps>0)
-
-G -
Print alignments in comments
-
-d=min-max -
Set default STS size
-
-r=+|- -
Enable/disable reverse STS lookup
-
-O=+|- -
Enable/disable syscall optimisation
-
-C=batchcnt -
Set number of STSes per batch
-
-o=outfile -
Set output file name
-
-q -
Quiet (no progress indicator)
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
Releases
Unchanged in 9 releases since Debian 5.0 (Lenny).