perlquestion
Anonymous Monk
Hi monks,
<p/>
I have at my work a little tricky task.
It is a string matching problem.
I want to compare two amino acid sequences (here in Letter code, single char represents one amino acid) to find at which positions one sequence lies in the other! example?
<code>
MAAGAAAAFAAAATTTTTTTTFTTTTTTTTTTTTAAAAEAAAARAAAAAA # 1. sequence
TTTTTTTTFTTTTTTTTTTTT # 2. sequence
result is: 2. lies at position 14 to 34 in 1.
</code>
simple?
new examples
<code>
SUBSTITUTION
AAAAEAAAARGAAATTTTFTTTTTTTTTTTTTTTTAAAAAAAAILVAAAAAAAA # 1. sequence
TTTTFTTTATTTTTTDTTTTT # 2. sequence
DELETION
AAAAAAAAAAAAATTGTTTTTTTXXXXXTTTTTTTTTTMAAAAAAAAAAAAAAAA # 1. sequence
TTGTTTTTTTTTTTTTTTTTM # 2. sequence
REVERSE
TTTTTTTTTTTTTTTTTTTT # 1. sequence
AAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAA # 2. sequence
PERFECT MATCHING ONLY AT BEGIN AND END OF 2. SEQUENCE
AAAAAAAAAAATTTTTTTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAAAAAA # 1.sequence
TTTTTTTTGGGNNGGGEEGGGEGGGGGGTTTTTTTTT # 2. Sequence
</code>
I tried with the regexp and the module String::Approx and aslice with the option 'minimal_distance', but I don't like the return values for this module.
<p/>
Any hints how to do "the best way"?
<p/>
Murcia
<p/>
<small><b>edit</b> (broquaint): dropped <tt><pre></tt> tags aand added formatting</small>
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