A fast shotgun assembly heuristic

Abstract

Genome sequencing opened a new era in genetics allowing the study of genomes at the nucleotide level. However, the chosen method of sequencing produced large numbers of nucleotide fragments which had to be re-assembled. The re-assembly of string fragments is known to be NP-hard. We report the results of our fast heuristic implementation for reassembling DNA fragments based on a unique approach to the problem called, "A Structured Pattern Matching Approach to Shotgun Sequence Assembly", (AMASS) created by Sun Kim. The algorithm's main idea is taken from the biological concept of probe hybridization where certain strands of nucleic acids are identified by short, unique sequences of bases that are contained within much longer DNA strands.