[BioC] Alignment viewer?

[Joern Toedling]

And in addition Biostrings has the functions consensusString and
consensusMatrix which, in combinantion with package seqLogo, can be used to
create a sequence logo from your multiple alignment in R.

Regards,
Joern

On Tue, 4 May 2010 16:30:04 -0700, 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