TFBS::...en::YMF(3pm)

✨ NAME ✨

TFBS::PatternGen::MEME — it's a pattern factory, bestie, and it runs the MEME program under the hood 💅

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🌸 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

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🦋 DESCRIPTION 🦋

Okay so TFBS::PatternGen::MEME builds position frequency matrices by calling out to an external program called MEME, which was written by Bailey and Elkan 🌟

Want the tea, the info, and the actual source code for MEME? It's all right here, no cap:

http://www.sdsc.edu/MEME

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💌 FEEDBACK 💌

Found a bug? Got opinions? Other comments? Please send bug reports and other comments to the author. They wanna hear from you fr fr 🫶

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👑 AUTHOR - Wynand Alkema 👑

Wynand Alkema <Wynand.Alkema@cgb.ki.se> — the icon who made this, periodt 💖

🌈 new 🌈

• Title: new
• Usage: my $patterngen = TFBS::PatternGen::YMF->new(%args);
• Function: the constructor for the TFBS::PatternGen::MEME object
• Returns: a TFBS::PatternGen::MEME 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 the meme executable. OPTIONAL: default 'meme'
• -additional_params — a string containing additional command-line switches for the meme program ✨

🎀 pattern, all_patterns, patternSet 🎀

These three methods listed above — pattern, all_patterns, and patternSet — are how you retrieve patterns, and they're common to all TFBS::PatternGen::* classes. So like, they're not special to this one, iykyk 💅

Please see TFBS::PatternGen for details 👑

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That's the whole vibe, bestie — this page is from perl v5.42.3, dated 2026-08-21, and it's literally called TFBS::...en::YMF(3pm) in the wild 🙈 tysm for reading, mwah 💋🌸