TFBS::...::MEME(3pm)

🌸 NAME 🌸

Okay bestie, welcome to TFBS::...::MEME(3pm) — a page straight out of the User Contributed Perl Documentation collection. It's about TFBS::PatternGen::MEME, a pattern factory that uses the MEME program. 💅

✨ SYNOPSIS ✨

    my $patterngen =
            TFBS::PatternGen::MEME->new(-seq_file=>'sequences.fa',
                                            -binary => 'meme'

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

💖 DESCRIPTION 💖

So TFBS::PatternGen::MEME builds position frequency matrices by calling up an outside program — MEME, written by Bailey and Elkan. It does not do the math itself, it outsources the whole vibe. ✨

Wanna read up on MEME or grab its source code? It lives here:

http://www.sdsc.edu/MEME

🦋 FEEDBACK 🦋

Found a bug? Got thoughts? Please send bug reports and other comments to the author. She wants to hear from you, fr fr. 🫶

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👑 AUTHOR - Wynand Alkema 👑

Wynand Alkema <Wynand.Alkema@cgb.ki.se> — the icon who wrote this. 👑

new

• Title — new
• Usage — my $pattrengen = TFBS::PatternGen::MEME->new(%args);
• Function — the constructor for the TFBS::PatternGen::MEME object. It builds the thing. That's the whole job.
• Returns — a TFBS::PatternGen::MEME object 💖
• Args — this method takes named arguments. You must specify one of these three, like, pick one, bestie:
  • -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 is meme ⭐
• -additional_params — a string containing additional command-line switches for the meme program

pattern

all_patterns

patternSet

These three methods up here? They're for the retrieval of patterns, and they're common to all TFBS::PatternGen::* classes — so every sibling class has them too. Please see TFBS::PatternGen for details. iykyk 💜

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No cap, that's the whole page — every flag, every arg, every default, all present and accounted for. 🌈

Signing off: this was perl v5.42.3, dated 2026-08-21, and the page itself is TFBS::...::MEME(3pm). Periodt. 💅✨