[Bioperl-l] Understanding LocatableSeq

[Ewan Birney]

On Tue, 4 Nov 2003, Wes Barris wrote:

> Ewan Birney wrote:
>
> >
> > On Tue, 4 Nov 2003, Wes Barris wrote:
> >
> >
> >>Hi,
> >>
> >>I am trying to create an msf alignment of several LocatableSeq objects.
> >>I have tried setting the "start" and "end" attributes of each LocatableSeq
> >>object before adding it to the alignment but the resulting sequences are
> >>still not aligned in the SimpleAlign object.  What am I doing wrong?
> >>
> >
> >
> > SimpleAlign does not automagically do the alignment - you need to call out
> > to Bio::Tools::Clustalw or TCoffee or something else. SimpleAlign
> > *represents* alignments, doesn't make them.
>
> I know that SimpleAlign does not automagically do the alignment.  That
> is why I am setting the "start" and "end" attributes.  I have an ACE
> file from clustal.  I am trying to write an msf file.  I have the
> sequences and the alignment information.  Now I want to write this
> into a SimpleAlign object.
>

Then you need to put pad characters (- or .) in the appropiate places
in the string of the LocatableSeq (in your case, it looks like the end).