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
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written
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Radhouane Aniba
This question has already been answered on biostar:
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.
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written
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Pierre Lindenbaum
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
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)
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What is your input data ? rsIDs (known SNPs) or nucleotide positions (novel SNPs from sequencing) ?