[Bioperl-l] Motifs and aligned sequences

Antonio genomewalker at gmail.com
Fri Aug 18 14:05:55 EDT 2006


Hello all,
I am trying to find the solution of this problem, I've tried several options
but no way. I want to find a motif in an aligned sequence, eg:
Aligned Sequence: -G---ATT---AT--ATA
Motif: ATTATA
So i want to find the motif inside this sequence  and return the last
position of the motif in the aligned sequence, in this case 16. I don't know
how I've to play with the '-', any suggestions?
Thanks in advance!
Antonio
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