Human PAML browser: a database of positive selection on human genes using phylogenetic methods

With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species....

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Bibliographic Details
Published in:Nucleic acids research 2008-01, Vol.36 (suppl-1), p.D800-D808
Main Authors: Nickel, Gabrielle C., Tefft, David, Adams, Mark D.
Format: Article
Language:English
Subjects:
Databases, Genetic
Genes
Genome, Human
Genomics
Humans
Internet
Likelihood Functions
Phylogeny
Proteins - genetics
Selection, Genetic
Sequence Alignment
User-Computer Interface
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Summary:With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood (ML) analysis of codon substitution models can be used to identify genes with an accelerated pattern of amino acid substitution on a particular lineage. However, the ML methods are computationally intensive and awkward to configure. We have created a database that contains the results of tests for positive selection along the human lineage in 13 721 genes with orthologs in the UCSC multispecies genome alignments. The Human PAML Browser is a resource through which researchers can search for a gene of interest or groups of genes by Gene Ontology category, and obtain coding sequence alignments for the gene and as well as results from tests of positive selection from the software package Phylogenetic Analysis by Maximum Likelihood. The Human PAML Browser is available at http://mendel.gene.cwru.edu/adamslab/pbrowser.py.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkm764