[Bioperl-l] Motifs and aligned sequences

Brian Osborne osborne1 at optonline.net
Fri Aug 18 17:52:44 EDT 2006


First remove the dashes from the consensus, s/-//g.

Brian O.

On 8/18/06 2:05 PM, "Antonio" <genomewalker at gmail.com> wrote:

> 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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