Non Coding, Synonymous Snp Prediction Tool ?

Question

[Radhouane Aniba]

Hi all,

I am trying to list all predictive tool that are able to predict : NON-CODING, SYNONYMOUS SNPs that are putatively causing disease.

Have you an idea on such tools names (with website if possible)

I have in my list

ANNOVAR ENSEMBL variation API (snp effect predictor tool) SNPnexus is-rSNP

Any idea is welcome

Thanks

Rad

[Khader Shameer]

What is your input data ? rsIDs (known SNPs) or nucleotide positions (novel SNPs from sequencing) ?

Answer 1

[Pierre Lindenbaum]

This question has already been answered on biostar:

• Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
• Finding Non-Synonymous Mutations
• Synonymous And Non-Synonymous Snps

however, I would like to cite this new database: dbNSFP ( http://sites.google.com/site/jpopgen/dbNSFP )

The dbNSFP is an integrated database of functional predictions from multiple algorithms for the comprehensive collection of human non-synonymous SNPs (NSs). Its current version (ver 1.0) is based on CCDS version 20090327 and includes a total of 75,931,005 NSs. It compiles prediction scores from four prediction algorithms (SIFT, Polyphen2, LRT and MutationTaster), a conservation score (PhyloP) and other related information.

[Pi]

Not sure i understand this comment - you can see on the screenshot (http://snpeff.sourceforge.net/) that it predicts all the consequences of a SNP that can currently be done reliably (i.e. it can say that a snp is synonymous or non synonymous but doesn't predict if the SNP is in something like an miRNA which is harder to delineate)

[Radhouane Aniba]

So in sum only snpEff is able to predict Synonymous SNPs ? no other predictors ? I am browsing the litterature actually it is hard to fine a paper clearly mentionning that.

Thx