FUZZNUC(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 FUZZNUC 💖

okay bestie, welcome to fuzznuc — a command line program from EMBOSS (that's "the European Molecular Biology Open Software Suite", the icon it is 💅). It lives in the "Nucleic:Motifs" command group(s), so that's the friend group it runs with. And fr fr? It searches for patterns in nucleotide sequences. That's the whole gig. And it ate. ✨

This page is the Debian manual for it, so let's get into it 🫶

✨ NAME ✨

fuzznuc — Search for patterns in nucleotide sequences 🌸

🦋 SYNOPSIS 🦋

fuzznuc -sequence seqall -pattern pattern -complement boolean
        -outfile report

fuzznuc -help

💜 DESCRIPTION 💜

fuzznuc is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Nucleic:Motifs" command group(s).

That's it, that's the summary. She's a motif-hunting girlie and she's booked and busy 💅

🎀 OPTIONS 🎀

🌸 Input section 🌸

  • -sequence seqall — the sequence(s) you're feeding in, bestie.
  • -pattern pattern — the pattern you're hunting for, and ngl this one comes with lore, so listen up 👑:

The standard IUPAC one-letter codes for the nucleotides are used. The symbol 'n' is used for a position where any nucleotide is accepted.

Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses '[ ]'. For example: [ACG] stands for A or C or G.

Ambiguities are also indicated by listing between a pair of curly brackets '{ }' the nucleotides that are not accepted at a given position. For example: {AG} stands for any nucleotides except A and G. (not me flipping the whole thing, but ok, we love a reverse queen 💀)

Each element in a pattern is separated from its neighbor by a '-'. (Optional in fuzznuc.)

Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: N(3) corresponds to N-N-N, N(2,4) corresponds to N-N or N-N-N or N-N-N-N. (slay, ranges ✨)

When a pattern is restricted to either the 5' or 3' end of a sequence, that pattern either starts with a '<' symbol or respectively ends with a '>' symbol. A period ends the pattern. (Optional in fuzznuc.)

For example, [CG](5)TG{A}N(1,5)C

That's the whole vibe check on patterns. iykyk 🧚

⭐ Advanced section ⭐

  • -complement boolean — Default value: N

💖 Output section 💖

  • -outfile report — where the results go, bestie 📝

😭 BUGS 😭

Found a bug? Don't suffer in silence, report it 💅

👑 SEE ALSO 👑

fuzznuc is fully documented via the tfm(1) system. Go read it, bestie, it's giving thorough 🌈

💜 AUTHOR 💜

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page.

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.

💖 okay that's the whole page, bestie. go fuzz some nucleotides, you're gonna eat 🫶✨

EMBOSS 6.4.0 · 05/11/2012 · FUZZNUC(1e) — periodt 💅🎀

📦 where this page comes from