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dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions.

Human mutation | Aug 27, 2011

With the advance of sequencing technologies, whole exome sequencing has increasingly been used to identify mutations that cause human diseases, especially rare Mendelian diseases. Among the analysis steps, functional prediction (of being deleterious) plays an important role in filtering or prioritizing nonsynonymous SNP (NS) for further analysis. Unfortunately, different prediction algorithms use different information and each has its own strength and weakness. It has been suggested that investigators should use predictions from multiple algorithms instead of relying on a single one. However, querying predictions from different databases/Web-servers for different algorithms is both tedious and time consuming, especially when dealing with a huge number of NSs identified by exome sequencing. To facilitate the process, we developed dbNSFP (database for nonsynonymous SNPs' functional predictions). It compiles prediction scores from four new and popular algorithms (SIFT, Polyphen2, LRT, and MutationTaster), along with a conservation score (PhyloP) and other related information, for every potential NS in the human genome (a total of 75,931,005). It is the first integrated database of functional predictions from multiple algorithms for the comprehensive collection of human NSs. dbNSFP is freely available for download at http://sites.google.com/site/jpopgen/dbNSFP.

Pubmed ID: 21520341 RIS Download

Mesh terms: Algorithms | Computational Biology | Databases, Nucleic Acid | Genetic Association Studies | Humans | Internet | Polymorphism, Single Nucleotide | Software

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Associated grants

  • Agency: NHLBI NIH HHS, Id: RC2 HL103010-01
  • Agency: NHLBI NIH HHS, Id: RC2 HL102419
  • Agency: NHLBI NIH HHS, Id: RC2-HL02419-01
  • Agency: CCR NIH HHS, Id: RC2 HL103010-01
  • Agency: NHGRI NIH HHS, Id: 1U01HG005728-01
  • Agency: CCR NIH HHS, Id: RC2 HL102419-01
  • Agency: NHGRI NIH HHS, Id: U01 HG005728
  • Agency: NHGRI NIH HHS, Id: U01 HG005728-01
  • Agency: NHLBI NIH HHS, Id: RC2 HL103010
  • Agency: NHLBI NIH HHS, Id: RC2 HL102419-01

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UCSC Genome Browser

A collection of genomes which include reference sequences and working draft assemblies, as well as a variety of tools to explore these sequences. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets. Also provided is a portal to the Encyclopedia of DNA Elements (ENCODE) and Neandertal projects.

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MutationTaster

Evaluates disease-causing potential of sequence alterations.

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