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      Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

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          Abstract

          The rate at which nonsynonymous single nucleotide polymorphisms (nsSNPs) are being identified in the human genome is increasing dramatically owing to advances in whole-genome/whole-exome sequencing technologies. Automated methods capable of accurately and reliably distinguishing between pathogenic and functionally neutral nsSNPs are therefore assuming ever-increasing importance. Here, we describe the Functional Analysis Through Hidden Markov Models (FATHMM) software and server: a species-independent method with optional species-specific weightings for the prediction of the functional effects of protein missense variants. Using a model weighted for human mutations, we obtained performance accuracies that outperformed traditional prediction methods (i.e., SIFT, PolyPhen, and PANTHER) on two separate benchmarks. Furthermore, in one benchmark, we achieve performance accuracies that outperform current state-of-the-art prediction methods (i.e., SNPs&GO and MutPred). We demonstrate that FATHMM can be efficiently applied to high-throughput/large-scale human and nonhuman genome sequencing projects with the added benefit of phenotypic outcome associations. To illustrate this, we evaluated nsSNPs in wheat ( Triticum spp.) to identify some of the important genetic variants responsible for the phenotypic differences introduced by intense selection during domestication. A Web-based implementation of FATHMM, including a high-throughput batch facility and a downloadable standalone package, is available at http://fathmm.biocompute.org.uk.

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          Most cited references 25

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          Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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            Human non-synonymous SNPs: server and survey.

             V. Ramensky (2002)
            Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human population DNA variation. One of the main goals of SNP research is to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases. Non-synonymous coding SNPs (nsSNPs) comprise a group of SNPs that, together with SNPs in regulatory regions, are believed to have the highest impact on phenotype. Here we present a World Wide Web server to predict the effect of an nsSNP on protein structure and function. The prediction method enabled analysis of the publicly available SNP database HGVbase, which gave rise to a dataset of nsSNPs with predicted functionality. The dataset was further used to compare the effect of various structural and functional characteristics of amino acid substitutions responsible for phenotypic display of nsSNPs. We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function of the protein, although it is insensitive to several other protein features considered. The strongest selective pressure was detected for proteins involved in transcription regulation.
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              A new generation of homology search tools based on probabilistic inference.

               Sean R. Eddy (2009)
              Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST's programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST's speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.
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                Author and article information

                Journal
                Hum Mutat
                Hum. Mutat
                humu
                Human Mutation
                Blackwell Publishing Ltd
                1059-7794
                1098-1004
                January 2013
                03 October 2012
                : 34
                : 1
                : 57-65
                Affiliations
                [1 ]Bristol Centre for Systems Biomedicine and MRC CAiTE Centre, School of Social and Community Medicine, University of Bristol Bristol, United Kingdom
                [2 ]Department of Computer Science, University of Bristol, The Merchant Venturers Building Bristol, United Kingdom
                [3 ]Institute of Medical Genetics, School of Medicine, Cardiff University Cardiff, United Kingdom
                [4 ]School of Biological Sciences, University of Bristol, Woodland Road Bristol, United Kingdom
                Author notes
                *Correspondence to: Tom Gaunt, Bristol Centre for Systems Biomedicine and MRC CAiTE Centre, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK. E-mail: Tom.Gaunt@ 123456bristol.ac.uk

                Communicated by Christophe Béroud

                [†]

                Joint first authorship.

                [‡]

                Joint last authorship.

                Contract grant sponsors: UK Medical Research Council (G1000427 to T.R.G. and I.N.M.D.); UK Biotechnology and Biological Sciences Research Council (BB/G022771 to J.G.); BIOBASE GmbH (to D.N.C. and P.D.S.).

                Article
                10.1002/humu.22225
                3558800
                23033316
                Copyright © 2012 Wiley Periodicals, Inc., A Wiley Company

                Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

                Categories
                Informatics

                Human biology

                hidden markov models, fathmm, snp

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