Smith-Waterman alignment algorithm is favored in search for siRNA off-target instead of the BLAST algorithm, because BLAST tends to overlook some significant homologous sequences, especially when they are short (21 nt~27 nt). Smith-Waterman algorithm, however, suffers from its own shortcomings, especially its inefficiency in searching through a large sequence database. This paper presents a two...

We investigate the use of variants of the Smith-Waterman algorithm to locate similarities in texts and in program source code, with a view to their application in the detection of plagiarism and collusion. The Smith-Waterman algorithm is a classical tool in the identification and quantification of local similarities in biological sequences, but we demonstrate that somewhat different issues aris...

1.0 Introduction Given a new protein sequence, scanning existing protein databases for similar sequences is becoming an important and repeated task in bioinformics. Initially, the Smith-Waterman [1] algorithm was developed to find local, optimal matches between an input sequence and a given database of existing protein sequences. The Smith-Waterman algorithm uses a recursive algorithm (dynamic ...

This paper summarizes the scientific legacy of Peter C. Waterman (1928–2012) who introduced concepts and theoretical techniques that have had a major impact on the fields of scattering by particles and particle groups, optical particle characterization, radiative transfer, and remote sensing. A biographical sketch is also included. & 2012 Elsevier Ltd. All rights reserved.

We present a probabilistic interpretation of local sequence alignment methods where the alignment scoring system (ASS) plays the role of a stochastic process defining a probability distribution over all sequence pairs. An explicit algorithms is given to compute the probability of two sequences given and ASS. Based on this definition, a modified version of the Smith-Waterman local similarity sea...

Physical maps can be constructed by "fingerprinting" a large number of random clones and inferring overlap between clones when the fingerprints are sufficiently similar. E. Lander and M. Waterman (Genomics 2: 231-239, 1988) gave a mathematical analysis of such mapping strategies. The analysis is useful for comparing various fingerprinting methods. Recently it has been proposed that ends of clon...

People often use similar usernames across different social media sites. This fact can be used to correlate accounts between different platforms. Since the first mention of this fact in 2009 no research has been done on how to exploit it most efficiently. We showed that ignoring the casing will most definitely improve the matching and we found that Smith-Waterman provides the best metric to matc...

The presented research work represent a highly robust and efficient parallel computing system development for biological gene sequencing. In this research work, the existing approaches has optimized the most optimum approach available till date in the form of Smithy Waterman algorithm for gene alignment or local gene sequencing. This paper mainly emphasizes on the system development for a trace...