[Genome] Vertebrate Multiz Alignment & Conservation

[Rachel Harte]

Hello Sirisha,

If you go to the description page for the conservation track, there are
different options that you can choose to configure the track. You can
reach this page by clicking on the blue/gray button at the left side of
the conservation track in the Genome Browser display or scroll down to the
"Comparative Genomics" group and click on the Conservation link above the
track control for this track. Once on the description page, you can check
the box for "Display bases identical to reference as dots" (in the
Multiple alignment base-level section). Then, when you zoom in to the
point where you see the nucletoides, those that are the same as the
reference will be shown as dots.

I hope that this helps you. Please let us know if you have further
questions.

Rachel


Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Sat, 28 Apr 2007, Pochareddy,  Sirisha wrote:

> Hi,
>
> I am trying to use the Vertebrate Multiz Alignment & Conservation track
> in the browser. I can see the alignment at the nucleotide level. But I
> am not able to find anyway to differentiate between identical
> nucleotides and others. Is there anyway I can color code aligned
> sequences (I did find the exon coloring useful, but even that does not
> differentiate between same and different bases)
>
> Thanks.
> Sirisha
>
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