Algorithms for finding transposons in gene sequences

Abstract

With the process of evolution, some genes will change their relative positions in gene sequence. These "jumping genes" are called transposons. Through some intuitive rules, we give a criterion to determine transposons among gene sequences of different individuals of the same species. Then we turn this problem into graph theory and give algorithms for different situations with acceptable time complexities. One of these algorithms has been reported briefly as the "iteration algorithm" in Kang et al.'s paper (in this paper, transposon is called "core-gene-defined genome organizational framework", cGOF). This paper provides the omitted details and discussions on general cases.Comment: 5 pages, 2 figure