Meta tools

Posted Fri, 11/09/2009 - 10:13 by Päivi Rosenström

Meta tools are tools which combine the analysis of several other prediction tools. Benefit of this is that the weaknesses of one program can be compensated by others and therefore the result is expected to be more reliable than obtained by individual programs. This page lists meta tools currently available.

Contents

Programs available
Description of programs
Useful databases
Review articles
Other articles
Useful links

Description of programs

PON-P

Pathogenic or NOT- pipeline is a meta tool that combines methods from the following categories: stability change prediction, aggregation prediction, disorder prediction and pathogenicity prediction. Inputs of the program can be given either as protein PDB code or FASTA formatted sequence and user can also include the list of mutations for analysis.

website: PON-P

Download:

Reference:

F-SNP

F-SNP is a meta tool spesifically prioritized for disease association studies. It uses in analysis 16 bioinformatics tools and databases. By using the tool one can make queries by using SNP ID, disease name, gene name or chromosomal region as an input. Output depends on analysis selected. By giving the SNP ID user gets information about its functional effects and by giving disease name the list of candidate gene list is given. A detailed description of meta tools function can be found from its website.

website: F-SNP

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Reference: Phil Hyoun Lee and Hagit Shatkay.F-SNP: computationally predicted functional SNPs for disease association studies.Nucleic Acids Res., January 2008; 36: D820 - D824. doi: http://dx.doi.org/10.1093/nar/gkm904

PolyDoms

PolyDoms is an integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations. Unlike other databases of similar nature, apart from integrating several coding SNPs (cSNPs) and protein-related information resources, we predict the implications of the non-synonymous SNPs (nsSNPs) using two well known algorithms (SIFT and PolyPhen).

website: PolyDoms

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Reference: Jegga et al. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res., 2007, 35, Database issue, D700-6. doi: 10.1093/nar/gkl826.

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MedRefSNP

MedRefSNP database provides integrated information about SNPs collected from the PubMed and OMIM databases. The RefSNP identifiers are automatically identified and are linked to various information sources such as the dbSNP, the HapMap database, the Entrez Gene database, the UCSC genome browser, the CGAP Pathway Searcher, and genetic association databases. And, each SNP is checked to determine whether the PolyDoms, SNPs3D or PolyPhen databases predicts that the SNP affects the phenotype of the protein encoded by the gene carrying the SNP. Also, neighboring SNPs showing strong linkage disequilibrium (LD) with published SNPs are included, using HapMap data