[Bioperl-l] alignment of 2 sequences/ FASTA

[Simon Chan]

Hi,

I would like to align 2 sequences.  Kind of hard to explain what I need
so I'll use an example:


seq 1: abab
seq 2: nnnnababnnnnn

How can I get the script to output that the match between
seq 1 and seq2 starts at position 5 and and ends at position 8?

I was told to run the FASTA program on the seq1 and seq2 and that
should get what I want, however, there doesn't seem to be a module
that will perform FASTA comparisons...?

Thanks, Everybody.

simon

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