Hello Perlmonks,

I have somewhat of a complicated (as far as I am concerned) pattern match problem that has me stumped.

For example, take two DNA strings, A and B. The letters w,x,y, and z can denote either A,T,G, or C
$A = ATGGAGTCGACGAATTTGAAGAAT
$B = xxxxxxATGGAGyxxxTCGAzxxxxCGAATTTGAAxxwGAAT
As you will notice, $A is contained within $B but is discontinous, separated by x's.
The basic premise is to use the sequence in $A and match this against the sequence of $B. In the process of doing this, each of the 'x' strings (4 in total) need to be extracted and categorized separately i.e. each on its own line (with an identifier # ideally).
The output from such a comparison would be;
xxxxxx
yxxx
zxxxx
xxw

I was trying some split stuff but got nowhere! Any help would be greatly! appreciated. I hope this makes sense.
Thanks,

Dr.J

In reply to Complicated pattern match by dr_jgbn

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