[Bioperl-l] alignment of 2 sequences/ FASTA

[Jonathan Barber]

On Tue, Feb 26, 2002 at 08:38:22AM -0800, Simon Chan wrote:
> 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...?

I don't think there are objects for manipulating FASTA data (I may
be wrong as I'm new to Bioperl), so it may be easier to use the BLAST
packages which will provide more or less the same results (the differences
lying in the heuristics that the BLAST and FASTA programs use).

> 
> Thanks, Everybody.
> 
> simon
> 
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-- 
Jon