Background: The accurate determination of orthology and inparalogy relationships is essential for comparative sequence analysis, functional gene annotation and evolutionary studies. Various methods have been developed based on either simple blast all-versus-all pairwise comparisons and/or time-consuming phylogenetic tree analyses.
Results: We have developed OrthoInspector, a new software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. In comparisons with existing methods, OrthoInspector improves detection sensitivity, with a minimal loss of specificity. In addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. The software has been used to study the orthology/in-paralogy relationships for a large set of 940,855 protein sequences from 59 different eukaryotic species.
Conclusion: OrthoInspector is a new software system for orthology/paralogy analysis. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert.