[BioC] Visualization of multiple alignments in bioconductor

[Martin Morgan]

"Schraga Schwartz" <Schragas at post.tau.ac.il> writes:

> Hello,
>
> I'm looking for a package/function which handles visualization of multiple
> sequence alignments. Does something like this exist in bioconductor?

Not exactly sure what you're looking for; here are a couple of
suggestions.

There's a package seqLogo that displays sequence 'logos' (variable
sized nucleotide letters based on weights) that could be used for
this.

The development version of ShortRead has, thanks to Simon Anders, a
function pileup that collates a large number of alignments into a
vector of the number of alignments overlapping each location in a
reference sequence. This could then be used with standard R graphics
packages, e.g., lattice, or exported to a genome browser with, e.g.,
rtracklayer.

I'm not sure about other visualization tools. These would be fun for
someone to develop, if they don't exist.

Martin

> Thanks,
>
>
>
> Schraga Schwartz
>
> Department of Human Molecular Genetics and Biochemistry,
> Tel Aviv University Medical School,
> Tel Aviv 69978, Israel.
> Tel: +972-3-640 6894
>
> email: schragas at post.tau.ac.il
>
>  
>
>
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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