Predicting Biologically Significant Snps

I am trying to figure out which SNP might change the structure and function of the translated protein based on the minor allele freq (MAF) >0.1 from 1000 genomes data and ensembl SIFT and Polychen scores. I am wondering if there are any other way of achieving the goal.

snp ensembl 1000genomes

• 3,263 views • link

updated 13.6 years ago by Zev.Kronenberg

• written 13.6 years ago by Pappu

2 answers

Check out the variant effect predictor. You can use it to get annotations from a number of functional effect prediction systems, such as Gerp and Consed.

• 3 views • link

written 13.6 years ago by Erik Garrison

The VAAST pipeline has a variant annotation tool (VAT). In addition the output can be used the GWAS tool VAAST.

• 1 views • link

written 13.6 years ago by Zev.Kronenberg

More posts like this

How does genenomestudio's genotyping module calculate minor allele frequency (Minor Freq)?
written 6.9 years ago by curious

I am playing around with genomestudio to do genotyping of 32 SNP arrays from human samples just to learn the technique One of my SNPs …
VEP vs webserver Polyphen scores
written 10.1 years ago by regrant •

Hello, I have recently noted a discrepancy the scores given by running PolyPhen at its [website][1] vs getting the PolyPhen score from ensembl's variant effect …
Forum: The Ensembl Vep For Easy Analysis Of Your Variants
written 12.6 years ago by Emily

The [Ensembl Variant Effect Predictor (VEP)][1] is a great way to analyse your own variation data. Available for free as [a simple web tool][2], and …
Analyzing The Expression And Regulation Of A Protein
written 13.5 years ago by Pappu

<p>I want to analyze all possible known mechanisms of regulation of gene expression and expression levels of a protein i.e. rhodopsin in normal cells and …