---
name: "bp_revtrans-motif"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_revtrans-motif"
---

# bp\_revtrans-motif(1p)

Reverse translate a Profam-like protein motif

## NAME

bp\_revtrans-motif - Reverse translate a Profam-like protein motif

## VERSION

Version 0.01

## SYNOPSIS

From a file:

```
    bp_revtrans-motif.pl -i motifs.txt
```

Using pipes:

```
   bp_revtrans-motif.pl < motifs.txt > output.txt
```

Using interactively at the command prompt:

```
   $ bp_revtrans-motif.pl
   MAAEEL[VIKP]
   1.   ATGGCNGCNGARGARYTNVHN
   [^P]H(IW){2,3}
   2.   NDNCAY(ATHTGG){2,3}
```

## DESCRIPTION

This script takes a protein motif as input and returns a degenerate oligonucleotide sequence corresponding to it. The main reason for doing this is to design degenerate primers that amplify a given sequence pattern.

The input motif consists of a string of one-letter residues, with any of the following syntactic elements:

- **\[...\]** : Redundant position.

  A position in which more than one residue is allowed. Example:

  ```
      [TS]YW[RKSD]
       ^^    ^^^^
  ```

- **\[^...\]** : Negated position.

  A position in which any residue is allowed, saved for those between brackets. Example:

  ```
      [^PW]MK[LAE]
        ^^
  ```

- **(...){n,m,...}** : Repeated motif.

  A motif that is repeated **n** or **m** times. It can have any of the previous syntactic elements. Example:

  ```
      A[SN]C(TXX){2,4,8}
             ^^^
  ```

The allowed letters are those that correspond to the 20 natural aminoacids, plus:

```
    B = N + D
    Z = Q + E
    X = All
```

## OPTIONS

### -i input-file:

A file with a list of motifs to reverse translate.

### -h

Display this help message.

## AUTHOR

Bruno Vecchi, `"vecchi.b at gmail.com"`

## BUGS

Please report any bugs or feature requests to `"vecchi.b at gmail.com"`

## COPYRIGHT & LICENSE

Copyright 2009 Bruno Vecchi, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.