[Bioperl-l] Motifs and aligned sequences

[Antoni Fernàndez-Guerra]

Thanks for you answer Brian, but I've already done it, the problem is that
if I remove the dashes I will lose the positions on the aligned sequence,
eg: s/-//g --->> GATTATATA, then if i want to know where is the last
position of the motif it will be 7 instead of 16. I want to know the
positions of the dashes too...but now I don't have any good idea, I will
keep working on it. Thanks again
Antonio

> A Divendres 18 Agost 2006 23:52, vàreu escriure:
> > Antonio,
> >
> > 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