---
name: "TFBS::PatternGen::AnnSpec"
section: "3pm"
platform: "linux"
package: "libtfbs-perl"
version: "0.7.1+ds-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/TFBS::PatternGen::AnnSpec"
---

# TFBS::PatternGen::AnnSpec(3pm)

a pattern factory that uses the AnnSpec program (version 2.1)

## NAME

TFBS::PatternGen::AnnSpec - a pattern factory that uses the AnnSpec program (version 2.1)

## SYNOPSIS

```
    my $patterngen =
            TFBS::PatternGen::AnnSpec->new(-seq_file=>'sequences.fa',
                                            -binary => 'ann-spec '
    my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
```

## DESCRIPTION

TFBS::PatternGen::AnnSpec builds position frequency matrices using an external program AnnSpec (Workman, C. and Stormo, G.D. (2000) ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Proc. Pacific Symposium on Biocomputing 2000).

## FEEDBACK

Please send bug reports and other comments to the author.

## AUTHOR - Wynand Alkema

Wynand Alkema \<Wynand.Alkema@cgb.ki.se\<gt\>

### new

```
 Title   : new
 Usage   : my $pattrengen = TFBS::PatternGen::AnnSpec->new(%args);
 Function: the constructor for the TFBS::PatternGen::AnnSpec object
 Returns : a TFBS::PatternGen::AnnSpec object
 Args    : This method takes named arguments;
            you must specify one of the following three
            -seq_list     # a reference to an array of strings
                          #   and/or Bio::Seq objects
              # or
            -seq_stream   # A Bio::SeqIO object
              # or
            -seq_file     # the name of the fasta file containing
                          #   all the sequences
           Other arguments are:
            -binary       # a fully qualified path to the 'meme' executable
                          #  OPTIONAL: default 'ann-spec'
            -additional_params  # a string containing additional
                                #   command-line switches for the
                                #   ann-spec program
```

### pattern

### all\_patterns

### patternSet

The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::\* classes. Please see TFBS::PatternGen for details.