Abstract:
: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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Nickel GC,Tefft D,Adams MDdoi
10.1093/nar/gkm764subject
Has Abstractpub_date
2008-01-01 00:00:00pages
D800-8issue
Database issueeissn
0305-1048issn
1362-4962pii
gkm764journal_volume
36pub_type
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