FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

Abstract

In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70–90)% for highly similar nucleotide sequences (> 80% similarity), and (54–70)% for sequences having (30–80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25–40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%–53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix

“…Up to now, numerous approaches have been proposed for comparing biological sequences, which can be subsumed under the apparatus of sequence alignment-based methods3456 and alignment-free methods. Sequence alignment-based method generally requires to define a sequence alignment scoring matrix and gap penalty parameters to represent the change of letters in the compared structures.…”

The identification of abrasive grains in the decohesion process by acoustic emission signal patterns

“…One of the techniques that makes it possible to find the optimum global match for two sequences is the Needleman-Wunsch algorithm [39]. This is often used in bioinformatics as one of the tools for finding the linearity of nucleotide or amino-acid sequences [40,41]. This algorithm, based on dynamic programming, can be easily adapted to the application being discussed.…”

Gpcodon Alignment: A Global Pairwise Codon Based Sequence Alignment Approach

“…In [17], an algorithm called PROVEAN (Protein Variation Effect Analyzer) was proposed, the proposed approach is a metric to compute the functional effect of variations, and it can be naturally applied to any variations of protein sequence. In [18], the authors presented a technique called FOGSAA that employs the famous branch and bound technique and is based on global pairwise sequence alignment. It builds a branch and bound tree where each node represents a comparison between two letters and each path represents a sequence alignment between two sequences.…”