InteGene: An Integer Linear Programming Tool for Discovering Approximate Gene Clusters

The opportunity of finding conserved segments in different species has increased with the increasing availability of completely sequenced genomes. Similarity of different parts or regions of different genomes suggests evolutionary relationships among different species and might foretell functional roles which prevented genes to separate. These similar segments are called conserved gene clusters or gene clusters. Approximate Gene Cluster Discovery Problem (AGCDP) is the problem of finding genes that are kept together in different species. Presented in this study is an Integer Linear Programming (ILP) formulation of the AGCDP. Since ILP is proven to be NP-complete, the study also made use of LP Relaxation since linear programming problems can be solved in polynomial time. The software used Java for the interface and other functionalities and R for solving ILP. InteGene, the tool produced by the study, can provide the user the best clusters given a set of data and input constraints which can be further tested for biological significance.