[R] looking for packages that visualize nucleotide sequence properties

[Martin Morgan]

The Bioconductor package 'geneplotter' might be useful,

http://bioconductor.org/packages/2.1/bioc/html/geneplotter.html

Martin

"Bernd Jagla" <baj2107 at columbia.edu> writes:

> Hi Jim,
>
> I don't have an explicit example. But, most genome browsers have something
> similar and much more sophisticated than what I am looking for: e.g.
> http://www.ensembl.org/Homo_sapiens/contigview?seq_region_right=158821424&se
> q_region_name=7&click_right=490&click_left=40&seq_region_left=1&seq_region_w
> idth=100000&vclick.x=20&vclick.y=131
> The problem I have with these representations is that they are all about ONE
> gene/region. I want to be able to see less information but for multiple
> genes. I haven't seen this for any of the data bases.
>
> Thanks for your kind help.
>
> Bernd
>
> |-----Original Message-----
> |From: Jim Lemon [mailto:jim at bitwrit.com.au]
> |Sent: Tuesday, November 27, 2007 5:30 AM
> |To: Bernd Jagla
> |Subject: Re: [R] looking for packages that visualize nucleotide sequence
> |properties
> |
> |Bernd Jagla wrote:
> |> Hi there,
> |>
> |> I am looking for R-packages that can help me visualize properties on
> |> nucleotide sequences. I want to display sequences in the 1-100K base
> |range
> |> as lines and plot features above and below those lines.
> |>
> |> Any ideas would be welcome.
> |>
> |Is there an example of what you want that we could view?
> |
> |Jim
>
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