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

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Mammalian genome sequencing is rapidly increasing, enabling large-scale evolutionary analyses.
• Phylogenetic analysis comparing substitution rates identifies genetic selection.
• Maximum-likelihood (ML) methods detect accelerated amino acid substitutions but are complex.

Purpose of the Study:

• To develop a user-friendly database for identifying human-specific positive selection.
• To provide researchers with easy access to gene-specific selection test results.

Main Methods:

• Created a database of positive selection test results for 13,721 human genes.
• Utilized UCSC multispecies genome alignments for ortholog identification.
• Implemented tests for positive selection using the Phylogenetic Analysis by Maximum Likelihood (PAML) software.

Main Results:

• The Human PAML Browser database contains comprehensive selection data for numerous genes.
• Researchers can search genes by name or Gene Ontology (GO) category.
• The browser provides coding sequence alignments and PAML test results.

Conclusions:

• The Human PAML Browser simplifies the study of human-specific evolutionary adaptations.
• This resource facilitates research into genes under positive selection in the human lineage.
• The tool enhances accessibility to complex phylogenetic analysis results.