---
name: "re-PCR"
section: "1"
platform: "linux"
package: "ncbi-epcr"
version: "2.3.12-1-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/re-PCR"
---

# re-PCR(1)

Find sequence tagged sites (STS) in DNA sequences

## NAME

re-PCR — Find sequence tagged sites (STS) in DNA sequences

## SYNOPSIS

**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 \[-g gaps\] \[-n mism\] \[-lq\] \[-m margin\] \[-O+\|-\] \[-C batchcnt\] \[-o outfile\] \[-r+\|-\] \[stsfile ...\]**

## DESCRIPTION

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)

## 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)](/famap/1.md) and [fahash(1)](/fahash/1.md)

## SEE ALSO

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

bioperl(1), e-pcr(1), [famap(1)](/famap/1.md) and [fahash(1)](/fahash/1.md)

## 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.