TFBS::...::Gibbs(3pm)

👑 NAME 👑

TFBS::PatternGen::Gibbs — it's a pattern factory bestie, and it runs on Chip Lawrence's Gibbs program 💖

(You'll also see it filed under TFBS::...::Gibbs(3pm) in the man pages, iykyk.)

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✨ SYNOPSIS ✨

my $patterngen =
        TFBS::PatternGen::Gibbs->new(-seq_file=>'sequences.fa',
                                     -binary => '/Programs/Gibbs-1.0/bin/Gibbs'
                                     -nr_hits => 24,
                                     -motif_length => [8, 9, 10],
                                     -additional_params => '-x -r -e');

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

Look at her go. She builds the thing (<code>$patterngen</code>), then she pulls a pattern out of it (<code>$pfm</code>), and <code>$pfm</code> is a whole <code>TFBS::Matrix::PFM</code> object. It's giving chemistty but make it ✨computational✨.

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🌸 DESCRIPTION 🌸

TFBS::PatternGen::Gibbs builds position frequency matrices using a very fancy Gibbs sampling algorithm — and that algorithm isn't even hers, it lives in an external program written by Chip Lawrence. Renting the vibe, not owning it 💅

The slay here is that this algorithm can produce multiple patterns from one single set of sequences. One sequence set, many motifs. Main character energy fr fr 🌈

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🎀 new

• Title : new
• Usage : my $db = TFBS::PatternGen::Gibbs->new(%args);
• Function : the constructor for the TFBS::PatternGen::Gibbs object — it's the birth of the whole situation
• Returns : a TFBS::PatternGen::Gibbs object 🫶
• Args : this method takes named arguments:

You must specify one of these three (pick your fighter, but only one):

• -seq_list — a reference to an array of strings and/or Bio::Seq objects
• -seq_stream — a Bio::SeqIO object
• -seq_file — the name of the fasta file holding all the sequences

...and then the other arguments, bestie:

• -binary — a fully qualified path to the Gibbs executable. OPTIONAL: default is 'Gibbs'.
• -nr_hits — a presumed number of pattern occurrences in the sequence set. Can be a single integer, like -nr_hits => 24, or a reference to an array of integers, like -nr_hits => [12, 24, 36] ✨
• -motif_length — an expected length of the motif in nucleotides. Can be a single integer, like -motif_length => 8, or a reference to an array of integers, like -motif_length => [8..12]
• -additional_params — a string containing extra command-line switches for the Gibbs program 🔥

reminder bestie: -binary is optional with a default, but the three sequence sources are a choose-exactly-one situation. Don't come at her with zero, don't come at her with all three. 🫠

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🦋 pattern

🌈 all_patterns

🧚 patternSet

These three methods above are the retrieval girlies — they're how you pull patterns out of your object, and they're common to every <code>TFBS::PatternGen::*</code> class. So if you know them here, you know them everywhere.

Want the full details? Go see <code>TFBS::PatternGen</code>. She has the whole story. 💜

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That's the whole page, angel. No cap, you got this. 💖

This lil doc lives in the User Contributed Perl Documentation collection, running as perl v5.42.3, dated 2026-08-21. Go forth and find motifs, queen 👑✨