A database of phylogenetically atypical genes in archaeal and bacterial genomes,identified using the <Emphasis Type="Italic">DarkHorse</Emphasis> algorithm |
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Authors: | Sheila Podell Terry Gaasterland Eric E Allen |
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Institution: | (1) Marine Biology Research Division, Scripps Institution of Oceanography University of California at San Diego, La Jolla, CA 92093, USA;(2) Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA |
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Abstract: | 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. |
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