[Bioperl-l] Allowing One error in Sequence matching

[Smithies, Russell]

How about chunk it into overlapping words, skip if >2 N, then regex?

$seq = "CGATCGNATGNCGTCTAGCTGACANGTTGACTCTAGCTGATCGATCGATCGTACGTANNCGTAGTCGTACNTACGATCTNACGCACGNATGCTACGTACG";

$motif = "ACGT";
foreach (split //, $motif) {$w .= "[${_}N]"}

foreach ($seq =~ /(?=(\w{4}))/g){
  next if tr/N/N/ >= 2;
  print "$_\n" if  eval "/$w/" ;
}



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap
> Sent: Thursday, 17 September 2009 9:42 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Allowing One error in Sequence matching
> 
> Hi All
> 
> I am not able to think of smart way to do sequence matching allowing
> userdefined number of mismatches.
> 
> For eg:
> 
> Given Sequence : AGCT will be considered a match to reference if any
> one base pair position #(1,2,3,4)  has a mismatch that is  [ACGTN] so
> the possible matches could be
> 
> This is for position 1.
> AGCT
> GGCT
> CGCT
> TGCT
> NGCT
> and likewise for each position.
> 
> any nice regular expression. One way that I could think was to
> generate all the possible tags for a given sequence and then do the
> matching. It will be a computationally expensive for long dataset .
> Any neat method ?
> 
> Thanks,
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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