LPI scores are inversely proportional to the phylogenetic distance between database match sequences and the query genome. These scores are useful not only for large-scalede novo predictions of horizontally transferred proteins, but can also serve as an independent quality control test for potential horizontal transfer candidates identified by alternative methods, especially those based on nucleic acid signatures. Candidates having high LPI scores are unlikely to have been horizontally transferred, since they are highly conserved among closely related organisms.

One unique and powerful feature of the DarkHorse HGT Candidate database is the opportunity to explore the phylogenetic background of potential HGT donors as well as recipients. The breadth of the database allows not only query sequences, but also their database match partners to be evaluated for sequence similarity or novelty compared to taxonomically related organisms.

DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A brief tutorial page is also available on-line.

Address of the bookmark: http://darkhorse.ucsd.edu/download.html