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Nucleic Acids Research Advance Access originally published online on October 25, 2007
Nucleic Acids Research 2008 36(Database issue):D800-D808; doi:10.1093/nar/gkm764
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Nucleic Acids Research, 2008, Vol. 36, Database issue D800-D808
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-com

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

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

Gabrielle C. Nickel, David Tefft and Mark D. Adams*

Department of Genetics, Case Western Reserve University, Cleveland, OH, USA

* To whom correspondence should be addressed. Tel: +1 216 368 2791; Fax: +1 216 368 3432; Email: markadams{at}case.edu or mda13{at}case.edu

Received August 15, 2007. Revised September 4, 2007. Accepted September 11, 2007.

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.

Present address: David Tefft, The Broad Institute, Cambridge, MA, USA.


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