amino acid number display in genome browser

[Bender, Ryan]

In using the in silico PCR tool to map amino acids that are present in a amplicon I am finding it difficult to determine what the amino acid number is. Is there a way to display the amino acid number of a UCSC gene that is present in an amplicon?  It’s getting frustrating having to cross reference the in silico browser with ensembl.

 

Thank you,

 

Ryan

[Pauline Fujita]

Hello Ryan,

The codon numbering would need to be based on one of the gene
prediction tracks. Presumably you're interested in the Ensembl track -
and if you have that track turned on you can set it to display the
amino acid numbering if you are zoomed to the right level and have the
visibility set accordingly.

You can read about the codon numbering feature here:

http://www.genome.ucsc.edu/goldenPath/help/hgCodonColoring.html

In particular, you will need to have codon coloring and number both
turned on, and the track must be zoomed to within 3 times the base
level.

To turn on codon numbering go to the Ensembl track description page -
for hg19 it's here:

http://www.genome.ucsc.edu/cgi-bin/hgTrackUi?g=ensGene

or for other assemblies you can click the gray bar to the left of the
Ensembl track in the main display or the track title above its
pulldown menu in the "Genes and Gene Prediction tracks" group. Once on
the display page, select:

Display mode: (anything but hide)
Color track by codons: genomic codons
Show codon numbering (on)

If you have further questions about the browser please feel free to
contact the mailing list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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