GENESIS: Genome Evolution Scenarios

GENESIS provides implementations of three algorithms:

1. The algorithm SwRT (Sorting by weighted reversals and transpositions) by Bader and Ohlebusch with quadratic running time.
2. The algorithm SRTl (Sorting by reversals, translocations, fusions, and fissions) by Hannenhalli and Pevzner with the improvements of Telser and Ozery-Flato and Shamir.
3. An algorithm for SwRTTl (Sorting by weighted reversals, translocations, transpositions, fusions and fissions) which combines the two algorithms SwRT and SRTl.

Webinterface for GENESIS.

SwRTTl produces a scenario consisting of 33 operation for  human vs. mouse (123 genes, data from the GRIMM Homepage, input file, output file) while an optimal scenario which only consists of reversals (produced with SRTl) consists of 35 operations.

SwRT produces a scenario consisting of 2 operations (1 reversal, 1 transpositions) between the mitochonrial genome of Drosophila melanogaster and Anopheles quadrimaculatus. (input file from the Mitochondrial Gene Arrangement Source Guide compiled by Jeffrey L. Boore) while an optimal scenario which only consists of reversals (produced with SRTl) consists of 4 operations.

The source code of the software is also available from the authos under the GPL v3.