title: OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs.
abstract: BACKGROUND
  The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time, discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface.
  
  
  RESULTS
  OrgConv (Organellar Conversion) is a computer package developed for detection of gene conversion between mitochondrial and chloroplast homologous genes. OrgConv is available in two forms; source code can be installed and run on a Linux platform and a web interface is available on multiple operating systems. The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. Most importantly, with the significantly reduced number of comparisons, the statistical power remains high in the face of correction for multiple tests.
  
  
  CONCLUSIONS
  Both the source code and the web interface of OrgConv are available for free from the OrgConv website http://www.indiana.edu/~orgconv. Although OrgConv has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences.
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405, USA. haoweilong@gmail.com
authors.forename: Weilong
authors.initials: W
authors.lastname: Hao
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D016384:Consensus Sequence / Q000235:genetics*; D030541:Databases, Genetic; D005785:Gene Conversion; D050259:Genes, Mitochondrial; D018745:Genome, Plant; D020407:Internet; D008928:Mitochondria / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D012984:Software