BP_REVTRANS-MOTIF(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

💫 BP_REVTRANS-MOTIF(1) 💫

okay bestie so this is a page from the User Contributed Perl Documentation, and honestly? it's a whole vibe. it's called bp_revtrans-motif and it's here to reverse translate a Profam-like protein motif. we're gonna get into it. 🧚

✨ NAME ✨

bp_revtrans-motif — reverse translate a Profam-like protein motif 🧬💅

🌸 VERSION 🌸

Version 0.01 — yes she's a baby, but she knows what she's doing.

🦋 SYNOPSIS 🦋

so there's like, three ways to run her. pick your fighter:

from a file:

bp_revtrans-motif.pl -i motifs.txt

using pipes:

bp_revtrans-motif.pl < motifs.txt > output.txt

using interactively at the command prompt:

$ bp_revtrans-motif.pl
MAAEEL[VIKP]
1.   ATGGCNGCNGARGARYTNVHN
[^P]H(IW){2,3}
2.   NDNCAY(ATHTGG){2,3}

🎀 DESCRIPTION 🎀

This script takes a protein motif as input and returns a degenerate oligonucleotide sequence corresponding to it. literally that's her whole job and she ate. 💅

The main reason for doing this is to design degenerate primers that amplify a given sequence pattern. iconic, honestly.

The input motif consists of a string of one-letter residues, with any of the following syntactic elements:

🔥 [...] : Redundant position

A position in which more than one residue is allowed. For example:

[TS]YW[RKSD]
 ^^    ^^^^

🔥 [^...] : Negated position

A position in which any residue is allowed, saved for those between brackets. For example:

[^PW]MK[LAE]
  ^^

🔥 (...){n,m,...} : Repeated motif

A motif that is repeated n or m times. It can have any of the previous syntactic elements. For example:

A[SN]C(TXX){2,4,8}
       ^^^

The allowed letters are those that correspond to the 20 natural aminoacids, plus:

  • B = N + D
  • Z = Q + E
  • X = All
bestie, remember X is all of them. all. every single one. she's not picky. 💀

🌈 OPTIONS 🌈

  • -i input-file — a file with a list of motifs to reverse translate. feed her the whole list, she's hungry. 🍓
  • -h — display this help message. the lil "help me help you" flag. 🫶

👑 AUTHOR 👑

Bruno Vecchi, vecchi.b at gmail.com — the mastermind, the main character. 🌟

🙈 BUGS 🙈

Please report any bugs or feature requests to vecchi.b at gmail.com — no cap, he wants to hear it. fr fr. 😭

Copyright 2009 Bruno Vecchi, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. slay. periodt. ✨

and that's the whole page, bestie 🎀 — brought to you by perl v5.42.3 and dated 2021-02-03, which is like, vintage in internet years but she still understood the assignment. 💜

📦 where this page comes from