On Tue, May 4, 2010 at 4:30 PM, Thomas Girke <thomas.girke@ucr.edu> wrote:

> If it helps, here are a few examples for handling multiple/pairwise
> alignments in Biostring's XStringSet container class and viewing them as
> html files in a browser (StringSet2html):
>
> http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Multiple-Sequence-Alignments-MSAs-
>
> It wouldn't be difficult to add color coding to this html-based viewing
> option.
>
> One question I would ask the developers of Biostrings is whether they
> are planning to release a specific object class for handling multiple
> alignments in the future.


This has been on the table for a while, I think. We need to initiate a more
serious discussion during this release cycle.

Michael


> For me XStringSet works just great for
> analyzing and manipulating multiple alignments..
>
> Thomas
>
>
> On Tue, May 04, 2010 at 03:33:19PM -0700, Erik Wright wrote:
> > Hi all,
> >
> > Does anyone know of a package that I can use to view alignments in R?
>  Basically I want to display a long DNAStringSet sequence by sequence:
> > Seq1:  ACTAGGAGCTYA...
> > Seq2:  ACTACGAGCTCA...
> > Seq3:  ACTAGGACCTNA...
> > etc....
> >
> > I just wanted to check if there is one already available so that I don't
> go off and reinvent the wheel.
> >
> > Thanks!,
> > Erik
> >
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