TFBS::...mplePFM(3pm)

🌸 NAME

TFBS::PatternGen::SimplePFM — a simple position frequency matrix factory, bestie 💖

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✨ 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

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🦋 DESCRIPTION

Okay so TFBS::PatternGen::SimplePFM does exactly what it says on the tin: it builds you a position frequency matrix out of a bunch of nucleotide sequences that are all the same length. That's the whole vibe check, no cap. 🧬

And the way you hand it those sequences? You've got options, bestie:

• as plain strings
• as Bio::Seq objects
• as a fasta file

Obsessed with the flexibility fr fr.

Heads up: this pattern generator always creates only one pattern from a given set of sequences. One set in, one pattern out. Periodt. 💅

🌟 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 object
• Args — this method takes named arguments, and you must specify one of these 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 📂

👑 pattern

👑 all_patterns

👑 patternSet

These three methods up above are your go-to for retrieving patterns, and they're common to all TFBS::PatternGen::* classes — so like, every sibling class has them too, iykyk. For the full tea, go check out TFBS::PatternGen 🫶

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and that's the whole page, bestie!! this little icon was cooked up as part of perl v5.42.3, dated 2026-08-21 — go forth and build matrices 💖✨🎀🦋🌸