---
name: "TFBS::PatternGen::SimplePFM"
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::SimplePFM"
---

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

a simple position frequency matrix factory

## NAME

TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory

## SYNOPSIS

```
    my @sequences = qw( AAGCCT AGGCAT AAGCCT
                        AAGCCT AGGCAT AGGCCT
                        AGGCAT AGGTTT AGGCAT
                        AGGCCT AGGCCT );
    my $patterngen =
            TFBS::PatternGen::SimplePFM->new(-seq_list=>\@sequences);

    my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
```

## DESCRIPTION

TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be passed either as strings, as Bio::Seq objects or as a fasta file.

This pattern generator always creates only one pattern from a given set of sequences.

### new

```
 Title   : new
 Usage   : my $db = TFBS::PatternGen::SimplePFM->new(%args);
 Function: the constructor for the TFBS::PatternGen::SimplePFM
            object
 Returns : a TFBS::PatternGen::SimplePFM obkect
 Args    : This method takes named arguments;
            you must specify one of the following
            -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
```

### pattern

### all\_patterns

### patternSet

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