UCSC Genome Browser on D. melanogaster Apr. 2006 (BDGP R5/dm3) Assembly
Jeffrey G. Scott
I would like to ask your help in use of the genome browser for the DGRP lines.
Specifically, what I am trying to do is evaluate how many non-synonymous SNPs are present in a gene, para in particular.
The browser is very helpful to see the various polymorphisms present in the DGRP lines, but I am not seeing any indication of whether the SNPs are synonymous or not. Is there any easy way to do this?
I can view at the base level, see the region with the SNP, locate this within the cDNA, translate and compare to the wild type, but there are so many SNPs that this seems horribly laborious.
I am hoping you can help me find an easier way.
Any ideas or suggestions would be most welcome. Thank you.
Jeffrey G. Scott
Professor
Department of Entomology
129 Garden Avenue
6134 Comstock Hall
Cornell University
Ithaca, NY 14853
Phone: 1-607-255-7340
Fax: 1-607-255-0939
http://blogs.cornell.edu/scott/
Matthew Speir
Thank you for your question about identifying non-synonymous variants using the UCSC Genome Browser.
If you have your variants in VCF, http://genome.ucsc.edu/goldenPath/help/vcf.html, or pgSNP, http://genome.ucsc.edu/FAQ/FAQformat.html#format10, format, then you can easily use the Variant Annotation Integrator (VAI) to accomplish this. The VAI allows you to upload your variants and then extract information about how these variants might affect the genes they intersect.
Before you go through the steps below, note that you will need to ensure that your variants are in VCF or pgSNP and uploaded to the Genome Browser as custom tracks: http://genome.ucsc.edu/cgi-bin/hgCustom?db=dm3.
Once you have formatted and uploaded your custom tracks, you can use the following steps to get this information from the VAI:
1. Navigate to the VAI for dm3, http://genome.ucsc.edu/cgi-bin/hgVai?db=dm3.
2. Select your variant tracks from the drop-down menu next to "variants".
3. Select the gene set you would like to use as a reference for your variants from the drop-down menu below "Select Genes".
4. Below "Functional Role", uncheck every box except "CDS - non-synonymous".
5. Select your output format (I recommend HTML as it is easier to read).
6. Click "Get results".
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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