[Bioperl-l] display sequence alignment

[Albert Vilella]

Yes, a PNG. Something as close as possible to the one attached, which
is a snapshot for the overview of a Jalview session. Jalview cannot be
scripted, so being able to programmatically produce this would be very
useful.

On Tue, Feb 16, 2010 at 4:59 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> I've done this by marking it up an alignment into HTML with colors, but no
> bioperl module for it that I know of. My way was pretty heavy (producing
> large files) but maybe a more compact CSS approach could produce smaller
> files.
>
> How else were you thinking of seeing this - in a PNG ?
>
> -jason
>
> Albert Vilella wrote:
>
> I am actually also interested in this :-)
>
> My requirements are to be able to define an image size, like 1200x800
> pixels, and then have a representation of the alignment produced
> through a script, with the clustalw or nucleotide colour palette like
> in Jalview.
>
> Anyone?
>
> On Tue, Feb 16, 2010 at 2:26 PM, Jessica Sun <jessica.sun at gmail.com> wrote:
>
>
> Do any one know how to display protein/peptide alignments in color using
> bioperl.
>
> thx
>
> On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun <jessica.sun at gmail.com> wrote:
>
>
>
> ---------- Forwarded message ----------
> From: Jessica Sun <jessica.sun at gmail.com>
> Date: Fri, Feb 12, 2010 at 8:44 PM
> Subject: one more question
> To: bioperl-l at lists.open-bio.org
>
>
> Does anyone knows how to get genomic(dna) sequences(with right sub regions)
> in gbk format when you only have NM_(mRNA) accession numbers.
>
> Thanks,
>
>
> --
> Jessica Jingping Sun
>
>
>
> --
> Jessica Jingping Sun
>
>
>
> --
> Jessica Jingping Sun
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