FUZZTRAN(1e)

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

💖 FUZZTRAN 💖

ok so bestie, welcome to fuzztran from the EMBOSS Manual for Debian — yes that's the 1e manual, we're in the general commands section, slay. Grab a strawberry 🍓 and let's get into it.

✨ NAME ✨

fuzztran — search for patterns in protein sequences (translated). yes the sequences get translated first, it's giving main character energy 🔥

🎀 SYNOPSIS 🎀

fuzztran -sequence seqall -pattern pattern [-frame list] [-table list]
         -outfile report

fuzztran -help

🦋 DESCRIPTION 🦋

So fuzztran is a command line program from EMBOSS, aka “the European Molecular Biology Open Software Suite” — iconic name, no notes 💅. It's part of the "Nucleic:Motifs,Protein:Motifs" command group(s). That's the whole description bestie, it's a short king 👑

🌸 OPTIONS 🌸

💜 Input section

  • -sequence seqall — your sequence input, literally what you're searching through 🫶
  • -pattern pattern — okay this one is a whole saga so sit down. The standard IUPAC one-letter codes for the amino acids are used. The symbol 'x' is used for a position where any amino acid is accepted. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses '[ ]'. For example: [ALT] stands for Ala or Leu or Thr. Ambiguities are also indicated by listing between a pair of curly brackets '{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met. Each element in a pattern is separated from its neighbor by a '-'. (Optional in fuzztran.) 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: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x. When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a '<' symbol or respectively ends with a '>' symbol. A period ends the pattern. (Optional in fuzztran.) For example, [DE](2)HS{P}X(2)PX(2,4)C ✨

🌈 Additional section

  • -frame list — Default value: 1 🎯
  • -table list — the translation table, and that's all she wrote 💅

👑 Output section

  • -outfile report — where your report lands, your moment of glory 📝

💀 BUGS 💀

If something's acting up (not in a cute way), bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). tell them bestie sent you 🫶

🔥 SEE ALSO 🔥

fuzztran is fully documented via the tfm(1) system. iykyk 📖

🧚 AUTHOR 🧚

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

  • Wrote the script used to autogenerate this manual page. not me being autogenerated 😭

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. respect the terms bestie, periodt ✋

fr fr, that's the whole page. go translate some sequences and find those patterns, you've got this 🌟

ok that's a wrap!! this was EMBOSS 6.4.0, dated 05/11/2012, and it ate, no cap 💅✨ bye bestie 🦋

📦 where this page comes from