title: Proteinortho: detection of (co-)orthologs in large-scale analysis.
abstract: BACKGROUND
  Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases.
  
  
  RESULTS
  The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes.
  
  
  CONCLUSIONS
  Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.
authors.affiliation: RNA Bioinformatics Group, Department of Pharmaceutical Chemistry, Philipps-University Marburg, Germany. lechner@staff.uni-marburg.de
authors.forename: Marcus
authors.initials: M
authors.lastname: Lechner
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiss
authors.forename: Lydia
authors.initials: L
authors.lastname: Steiner
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012984:Software