BP_REVTRANS-MOTIF(1p)

💖 BP_REVTRANS-MOTIF 💖

okay bestie so this is bp_revtrans-motif (from the 1p manual, Perl user-contributed docs section, iykyk) — it's the little script that reverse translates a Profam-like protein motif. and yes it eats, we'll get there.

✨ VERSION ✨

Version 0.01 🎀 (baby version, still iconic)

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🌸 SYNOPSIS 🌸

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}

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🦋 DESCRIPTION 🦋

so basically? you hand this script a protein motif, and it hands you back a degenerate oligonucleotide sequence for it. the whole point, the main character reason for existing, is designing degenerate primers that amplify a given sequence pattern. periodt. 💅

The input motif is a string of one-letter residues, and it can have any of these syntactic elements:

• [...] : Redundant position. A position in which more than one residue is allowed. Example:

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

• [^...] : Negated position. A position in which any residue is allowed, saved for those between brackets. 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. 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

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🎀 OPTIONS 🎀

• -i input-file — A file with a list of motifs to reverse translate.
• -h — Display this help message.

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👑 AUTHOR 👑

Bruno Vecchi, "vecchi.b at gmail.com" 🫶

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💀 BUGS 💀

Please report any bugs or feature requests to "vecchi.b at gmail.com"

not me telling you to email Bruno directly but like… that's literally what it says bestie 😭

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🌈 COPYRIGHT & LICENSE 🌈

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.

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and that's the whole page fr fr — this was perl v5.32.1, dated 2021-08-15, and it's the BP_REVTRANS-MOTIF(1p) manual. go reverse translate something cute. slay 💖✨