TFBS::...::Elph(3pm)

✨ NAME ✨

TFBS::PatternGen::Elph — a pattern factory that uses the Elph program 💅

(oh and btw this lives in the User Contributed Perl Documentation, page name TFBS::...::Elph(3pm) — hi bestie 🫶)

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🌸 SYNOPSIS 🌸

my $patterngen =
        TFBS::PatternGen::Elph->new(-seq_file=>'sequences.fa',
                                     -binary => '/Elph/elph'
                                     -motif_length => [8, 9, 10],
                                     -additional_params => '-x -r -e');

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

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💖 DESCRIPTION 💖

okay so here's the lore, straight from the docs: TFBS::PatternGen::Gibbs builds position frequency matrices using an advanced Gibbs sampling algorithm implemented in an external Gibbs program by Chip Lawrence. (yes bestie, the page says Gibbs, we're just relaying the tea ☕ no cap.) The algorithm can produce multiple patterns from a single set of sequences, which is lowkey iconic 🌈

🎀 new 🎀

• Title: new
• Usage: my $db = TFBS::PatternGen::Gibbs->new(%args);
• Function: the constructor for the TFBS::PatternGen::Gibbs object
• Returns: a TFBS::PatternGen::Gibbs object
• Args: this method takes named arguments — and 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 Gibbs executable. OPTIONAL: default 'Gibbs'
• -nr_hits — a presumed number of pattern occurrences in the sequence set. it can be a single integer, e.g. -nr_hits => 24, or a reference to an array of integers, e.g. -nr_hits => [12, 24, 36]
• -motif_length — an expected length of motif in nucleotides. it can be a single integer, e.g. -motif_length => 8, or a reference to an array of integers, e.g. -motif_length => [8..12]
• -additional_params — a string containing additional command-line switches for the Gibbs program

👑 pattern

👑 all_patterns

👑 patternSet

These three methods — pattern, all_patterns, and patternSet — are used for the retrieval of patterns, and they're common to all TFBS::PatternGen::* classes. Please see TFBS::PatternGen for details 🫶

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and that's the whole page bestie, you ate it, periodt 💅

this was perl v5.42.3, dated 2026-08-21, and the page is TFBS::...::Elph(3pm) — mwah, go slay some motifs 💖✨