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How To Get All Different Variants Of A Peptide?

I have a peptide like this

SNINNIING

Let's suppose that for 2 of the positions I have alternative amino acids. For example, the first "S" could be "T" and the last "G" could be "E". This means that I can have 3 alternative peptides

TNINNIING (S -> T)
SNINNIINE (G -> E)
TNINNIINE (both)

Is there a way to get these additional peptides using Perl? My problems begin when I have 3 or more alternative amino acids, because otherwise I could it by hand!

perl
• 4,095 views • link
updated by Woa Woa • written by Panos Panos

The title of your question suggests that you want to know how to permute any peptide sequence to any other sequence of the same length. Is that correct?

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written by Neilfws Neilfws

Yes, but the permutations are not random. I know that, for example I only have T instead of S. It's like I have a peptide with ambiguities 

  [TS]NINNIIN[GE]

and want to obtain all 4 possible combinations.

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written by Panos Panos

Not related to the question, but I can't see your entire comment Neilfws... If I go to my profile and then to messages, I see sentences that I can't see here.

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written by Panos Panos

Yes; original comment was different, I edited it but the old one still shows in message feeds. I don't know why.

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written by Neilfws Neilfws

2 answers

Check if this thread helps:

http://stackoverflow.com/questions/10665538/perl-generate-all-matching-string-to-a-regex

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written by Woa Woa

use strict; use warnings; use Regexp::Genex qw(:all); my $regex="(T|S)NINNIIN(G|E)"; print $_,"\n" for strings($regex);

produces the following output:

TNINNIING
TNINNIINE
SNINNIING
SNINNIINE
• 0 views • link
updated by Neilfws Neilfws • written by Woa Woa

I wonder why this code formats correctly in preview but not when posted?

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written by Neilfws Neilfws

Thanks Woa! I installed the module and worked like a charm!

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written by Panos Panos

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