A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm

Background: The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. DarkHorse, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI) ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not. Description: The DarkHorse algorithm has been applied to 955 microbial genome sequences, and the results organized into a web-searcha...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Sheila Podell, Terry Gaasterland, Eric E. Allen
• Keywords: Amino Acid Sequence, BMCBI 2008, Genomes, Lpi Scores