The term orthologous segments is defined as a set of genomic segments in different organisms descended from a common ancestor without large rearrangements. In comparative genomics, the accurate detection of orthologous segments (also referred to as syntenic segments or syntenies) plays a key role, as it is essential for the following.
- Inference of the rearrangement-based phylogenies.
- Reconstruction of the ancestral genomes.
- Computation of the whole genome alignments.
- Identification of the orthologous genes.
- Detection of the non-coding functional elements such as regulatory elements.
The problem of identifying orthologous segments is referred to as orthology mapping.
OSfinder (Orthologous Segment finder) performs accurate orthology mapping by using Markov chain models and machine learning techniques. The originality of OSfinder lies in the ability to compare multiple genomes simultaneously, and to automatically optimize the parameters used in the Markov chain models, while the users of the other existing orthology mapping programs suffer from the manual setting of the parameter values.
Input and Output
OSfinder takes the genomic locations of anchors as input, and reports the genomic locations of chains and orthologous segments as output.
Anchor -- The term anchor generally refers to well-conserved short regions between two or multiple genomes, and is biologically defined as a group of homologous genes or a set of homologous sequence matches.
Chain -- The term chain is defined as a set of genomic segments in which anchors are distributed densely in off-diagonal positions.
Orthologous Segment -- The term orthologous segment is defined as a set of genomic segments in different organisms descended from a common ancestor without large rearrangements.