PT - JOURNAL ARTICLE AU - Hongyi Xin AU - Jeremie Kim AU - Sunny Nahar AU - Can Alkan AU - Onur Mutlu TI - LEAP: A Generalization of the Landau-Vishkin Algorithm with Custom Gap Penalties AID - 10.1101/133157 DP - 2017 Jan 01 TA - bioRxiv PG - 133157 4099 - http://biorxiv.org/content/early/2017/05/07/133157.short 4100 - http://biorxiv.org/content/early/2017/05/07/133157.full AB - Motivation Approximate String Matching is a pivotal problem in the field of computer science. It serves as an integral component for many string algorithms, most notably, DNA read mapping and alignment. The improved LV algorithm proposes an improved dynamic programming strategy over the banded Smith-Waterman algorithm but suffers from support of a limited selection of scoring schemes. In this paper, we propose the Leaping Toad problem, a generalization of the approximate string matching problem, as well as LEAP, a generalization of the Landau-Vishkin’s algorithm that solves the Leaping Toad problem under a broader selection of scoring schemes.Results We benchmarked LEAP against 3 state-of-the-art approximate string matching implementations. We show that when using a bit-vectorized de Bruijn sequence based optimization, LEAP is up to 7.4x faster than the state-of-the-art bit-vector Levenshtein distance implementation and up to 32x faster than the state-of-the-art affine-gap-penalty parallel Needleman Wunsch Implementation.Availability We provide an implementation of LEAP in C++ at github.com/CMU-SAFARI/LEAP.Contact hxin{at}cmu.edu, calkan{at}cs.bilkent.edu.tr or onur.mutlu{at}inf.ethz.ch