TFBS::...AnnSpec(3pm)

✨ NAME ✨

okay bestie, welcome to TFBS::...AnnSpec(3pm) — it's the manual page for TFBS::PatternGen::AnnSpec, which is a pattern factory that uses the AnnSpec program (version 2.1). no cap, that's the whole vibe 💅

---

🦋 SYNOPSIS 🦋

    my $patterngen =
            TFBS::PatternGen::AnnSpec->new(-seq_file=>'sequences.fa',
                                            -binary => 'ann-spec '

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

(yes, that first call is missing a closing paren in the original — i'm not touching it, i'm just the messenger 🫶)

---

💖 DESCRIPTION 💖

so what does TFBS::PatternGen::AnnSpec actually do? it builds position frequency matrices using an external program called AnnSpec. that's the main character of this whole page, and if you wanna cite it (and you should, it's iconic), here's the receipt:

Workman, C. and Stormo, G.D. (2000) ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Proc. Pacific Symposium on Biocomputing 2000.

periodt. ✨

---

🌸 FEEDBACK 🌸

found a bug? got thoughts? please send bug reports and other comments to the author. they want to hear from you, fr fr 💌

---

👑 AUTHOR — Wynand Alkema 👑

Wynand Alkema <Wynand.Alkema@cgb.ki.se<gt>

---

new

• Title: new
• Usage: my $pattrengen = TFBS::PatternGen::AnnSpec->new(%args);
• Function: the constructor for the TFBS::PatternGen::AnnSpec object. it makes the thing. that's the function. 🌱
• Returns: a TFBS::PatternGen::AnnSpec object
• Args: this method takes named arguments. and ngl, 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 is 'ann-spec' (yes bestie, the description says 'meme', we're just reporting the lore exactly as it's written 🙈)
• -additional_params — a string containing additional command-line switches for the ann-spec program

---

pattern

all_patterns

patternSet

so these three methods up here — pattern, all_patterns and patternSet — are the ones you use for the retrieval of patterns, and they're common to all the TFBS::PatternGen::* classes. like, every single one of them shares this energy. head over to TFBS::PatternGen for the details 👑

---

that's the whole page, bestie. this one's from perl v5.42.3, dated 2026-08-21, filed under TFBS::...AnnSpec(3pm). go build some matrices, slay, and remember: the vibe changes, the facts never do 💜🎀🦋