BMCBI
2006
13 years 4 months ago
2006
Background: Detecting remote homologies by direct comparison of protein sequences remains a challenging task. We had previously developed a similarity score between sequences, cal...
BMCBI
2008
13 years 4 months ago
2008
Background: Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more t...
FPL
2008
Springer
13 years 6 months ago
2008
Springer
Wavefront algorithms, such as the Smith-Waterman algorithm, are commonly used in bioinformatics for exact local and global sequence alignment. These algorithms are highly computat...
FPL
2003
Springer
13 years 9 months ago
2003
Springer
With an aim to understand the information encoded by DNA sequences, databases containing large amount of DNA sequence information are frequently compared and searched for matching ...
ISPDC
2007
IEEE
13 years 10 months ago
2007
IEEE
Whole genome comparison consists of comparing or aligning genome sequences with a goal of finding similarities between them. Previously we have shown how SIMD Extensions used in ...
IPPS
2008
IEEE
13 years 11 months ago
2008
IEEE
One of the most commonly used tools by computational biologists is some form of sequence alignment. Heuristic alignment algorithms developed for speed and their multiple results s...
BIBE
2008
IEEE
13 years 11 months ago
2008
IEEE
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
SASP
2009
IEEE
13 years 11 months ago
2009
IEEE
—This paper describes a multi-threaded parallel design and implementation of the Smith-Waterman (SM) algorithm on compute unified device architecture (CUDA)-compatible graphic pr...
RECOMB
2001
Springer
14 years 4 months ago
2001
Springer
The Smith-Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach w...