convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters

lrl1997 has asked for the wisdom of the Perl Monks concerning the following question:

I would like to use perl script to convert all ambiguous letters (R, Y, K, M, S etc) in a DNA sequence to all possible non-ambiguous letters.

For example,

to convert sequence "ARGBCTC" to:

AAGCCTC

AAGGCTC

AAGTCTC

AGGCCTC

AGGGCTC

AGGTCTC

However, there are so many different combinations (let's say only 2 ambiguous letter maximum in one sequence, how to do this in an efficient way??????????// Could anyone point me to the right direction?

Thank you.

Comment on convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters

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Re: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters by BrowserUk (Patriarch) on Feb 16, 2013 at 01:29 UTC
For strings with upto say a half a dozen or so wildcards, glob does this quite efficiently: `$in = 'ARGBCTC';; $in =~ s[[^ACGT]][{A,C,G,T}]g;; print $in;; A{A,C,G,T}G{A,C,G,T}CTC print for glob $in;; AAGACTC AAGCCTC AAGGCTC AAGTCTC ACGACTC ACGCCTC ACGGCTC ACGTCTC AGGACTC AGGCCTC AGGGCTC AGGTCTC ATGACTC ATGCCTC ATGGCTC ATGTCTC` [download] With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply] [d/l]
Re^2: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters by 7stud (Deacon) on Feb 16, 2013 at 02:55 UTC
Gee whiz. That's clever.	[reply]
Re^2: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters by lrl1997 (Novice) on Feb 18, 2013 at 23:49 UTC
so smart!!!! Thank you indeed!!!	[reply]
Re: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters by AnomalousMonk (Archbishop) on Feb 16, 2013 at 04:28 UTC
Also see section 4.3.2 "Genomic Sequence Generator" of Dominus's excellent Higher Order Perl available for free download here.	[reply]