[BioC] Alignment viewer?

[Thomas Girke]

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. 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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