re-PCR (1)

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 ...]

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.

-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)

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 fahash(1)

/usr/share/doc/ncbi-epcr/README.txt

bioperl(1), e-pcr(1), famap(1) and fahash(1)

This manual page was written by Andreas Tille <[email protected]> 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.