I'm confused about what you want (update: please remember this is PerlMonks and not BioMonks), but a part of it seems to be a permutation of all the other middle, single-base possibilities given the one that is actually present. If so, maybe something like this: 

c:\@Work\Perl\monks>perl -wMstrict -le
"my $ppi_pm_seq = 'ACTGCCT';
 ;;
 my $n = 3;
 ;;
 my $extraction =
 my ($before, $mid, $after) =
 $ppi_pm_seq =~ m{ \A (.{$n}) (.) (.{$n}) \z }xms;
 ;;
 die qq{no extraction from '$ppi_pm_seq'} unless $extraction;
 ;;
 my ($ppi_pm_id, $ppi_mm_id, $mpi_pm_id, $mpi_mm_id) =
   map qq{$before$_$after},
   $mid, grep $_ ne $mid,
   qw(A T C G)
   ;
 ;;
 print qq{'$_'} for $ppi_pm_id, $ppi_mm_id, $mpi_pm_id, $mpi_mm_id;
"
'ACTGCCT'
'ACTACCT'
'ACTTCCT'
'ACTCCCT'

[download]
Note that the  $ppi_pm_id permuted sequence is the same as the "input"  $ppi_pm_seq sequence (if that's what you want).

Update 1: Note also that the simpler  (.{$n}) (.) or  (.{n}) (.) expressions suffice if you can guarantee, as an initial step, that your input strings are only  A T C G characters. This can be as simple as (tested): 

my $s = 'ATCGxTGAC';
my $foreign = $s =~ tr/ATCG//c;
print qq{foreign character in '$s'} if $foreign;

[download]

Update 2: An interesting side note: If you have Perl version 5.10+ available, you can use the  (?-PARNO) relative recursive subpattern regex extension to (perhaps) simplify things a bit (tested):
    m{ \A (.{$n}) (.) ((?-3)) \z }xms;
in place of
    m{ \A (.{$n}) (.) (.{$n}) \z }xms;
(I rather doubt this alteration would speed things up significantly, but I've not done any testing; it's just a thought.)

Give a man a fish:  <%-{-{-{-<

In reply to Re: DNA Pattern Matching by AnomalousMonk
in thread DNA Pattern Matching by Speed_Freak

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