gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences

Abstract

Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods applied to this problem. We introduce gpALIGNER, a fast pairwise DNA-DNA global alignment algorithm. gpALIGNER uses similar score schema with DIALIGN-T to produce the final alignment. It also uses the concept of “spaced seeds” to determine locally aligned subsequences which construct semi-global alignment as the preliminaries of global alignment computation. This enables gpALIGNER to have the precision provided by the DIALIGN-T algorithm in considerably less time and space complexities. We performed benchmarking of our approach based on numerous datasets from standard benchmarking databases and real sequences of NCBI database where gpALIGNER performed three times faster than DIALIGN-T. gpALIGNER is a new alternative for having sensitivity and selectivity of DIALIGN-T but with less computational cost.

Keywords

• sequence alignment
• pairwaise alignment
• sequence comparison
• dynamic programming
• spaced seeds