How To Get All Different Variants Of A Peptide?

Question

[Panos]

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!

[Neilfws]

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?

[Panos]

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.

[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.

[Neilfws]

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

Answer 1

[Woa]

Check if this thread helps:

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

Answer 2

[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

[Neilfws]

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

[Panos]

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