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PMID: 17274820 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

DarkHorse: a method for genome-wide prediction of horizontal gene transfer.

Genome biology ·Vol. 8 ·No. 2 ·2007-00-00 ·Pages R16

Podell S, Gaasterland T

Abstract

A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.

MeSH Terms
Algorithms Computational Biology/methods Databases, Genetic Gene Transfer, Horizontal/genetics Genomics/methods Phylogeny Probability Software
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Podell Sheila
Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA. spodell@ucsd.edu
Gaasterland Terry
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2007-8-2-r16
Email
spodell@ucsd.edu
Published
2007-00-00
Pages
R16
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1852411
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2007-8-2-r16 PMC Full Text View journal details
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