[BioC] Alignment viewer?

[Erik Wright]

Very good idea!  Thanks Thomas!


On May 4, 2010, at 4:30 PM, Thomas Girke 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. 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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