Gene Verification and Discovery by Walking Tree Method

The Walking Tree Method [3, 4, 5, 18] is an approximate string alignment method that can handle insertions, deletions, substitutions, translocations, and more than one level of inversions all together. Moreover, it tends to highlight gene locations, and helps discover unknown genes. Its recent improvements in runtime and space use extends its capability in exploring large strings. We will briefly describe the Walking Tree Method with its recent improvements [18], and demonstrate its speed and ability to align real complete genomes such as Borrelia burgdorferi (910724 base pairs of its single chromosome) and Chlamydia trachomatis (1042519 base pairs) in reasonable time, and to locate and verify genes.