Bioinformatics
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Tag: Sequence Alignment :: GPGPU.org
Abstract: In this paper, we propose a fine-grained cycle sharing (FGCS) system capable of exploiting idle graphics processing units (GPUs) for accelerating sequence homology search in local area network environments. Our system exploits short idle periods on GPUs by running small parts of guest programs such that each part can be completed within hundreds of milliseconds.
M i c r o b e s . n l
"Any one who considers arithmetical methods of producing random digits is, of course, in a state of sin.
Sequence Alignment Techniques are very useful in the field of Bioinformatics.
Sequence Alignment Techniques
Background on Nucleic Acid Dot Plots
Dot plots provide a simple, yet extremely powerful means of nucleic acid sequence analysis. Most commonly they are examined to identify one of two situations: The principle used to generate dot plots is straightforward.List of sequence alignment software - Wikipedia, the free encyclopedia
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment .
Features
JAligner: Java implementation of the Smith-Waterman algorithm for biological sequence alignment
FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985. [ 1 ] Its legacy is the FASTA format which is now ubiquitous in bioinformatics .
FASTA - Wikipedia, the free encyclopedia
Smith–Waterman algorithm - Wikipedia, the free encyclopedia
The Smith–Waterman algorithm is a well-known algorithm for performing local sequence alignment ; that is, for determining similar regions between two nucleotide or protein sequences .
In computer science , Hirschberg's algorithm , named after its inventor, Dan Hirschberg , is a dynamic programming algorithm that finds the least cost sequence alignment between two strings , where cost is measured as Levenshtein distance , defined to be the sum of the costs of insertions, replacements, deletions, and null actions needed to change one string to the other.
Hirschberg's algorithm - Wikipedia, the free encyclopedia
The Needleman–Wunsch algorithm performs a global alignment on two sequences (called A and B here).
Needleman–Wunsch algorithm - Wikipedia, the free encyclopedia
Sequence alignment - Wikipedia, the free encyclopedia
In bioinformatics , a sequence alignment is a way of arranging the sequences of DNA , RNA , or protein to identify regions of similarity that may be a consequence of functional, structural , or evolutionary relationships between the sequences. [ 1 ] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix .In bioinformatics , B asic L ocal A lignment S earch T ool, or BLAST , is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences .