[Genome] Mapping SNP and protein

[Kayla Smith]

Helix,

Unfortunately, we do not currently have a way to generate the protein
sequence with changed amino acids where the SNPs in the genomic sequence
are located.  This is a feature we would like to implement sometime this
year, however.

In the meantime, you might at least find the 'func' field of the SNP
tables useful.  The function 'coding-nonsynon' denotes SNPs in coding
regions where the peptide will be changed (this info is provided by
dbSNP).

Use the Table Browser with the following options:

clade: Vertebrate
genome: Human
assembly: Mar. 2006
group: Variation and Repeats
track: SNPs(126)
table: snp126
region: select the "position" button and paste in chr17:76705160-76721740

output format:  "selected fields from primary and related tables"

on the next page select: chrom, chromStart, chromEnd, name, func.

click "get output"

Your results will have your SNP's rs numbers, positions and some 
information about the amino acids they make.  I see one SNP in your list 
that is labeled as "coding-nonsynon".

You might also be interested in some previously answered mailing list 
questions on this topic:

https://www.soe.ucsc.edu/pipermail/genome/2007-May/013638.html
https://www.soe.ucsc.edu/pipermail/genome/2007-May/013684.html

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group




Helix Photon wrote:
> Hi,
> I am interested in the number of SNP present in the following genomic coordinate chr17:76705160-76721740 and when I queried through the Table browser, I got 63 hits.
> Now my question is:
> a) Like in dbSNP, can I get the information about the amino acid change and weather SNP is present near 3' or 5' position of the coordinate.
> b) If I need to use intersection between the tables for this, which tables to look for the protein information.
> 
> thanks
> 
> 
> 
>        
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