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Therefore, the BLAST algorithm uses a heuristic approach that is less accurate than the Smith-Waterman algorithm but over 50 times faster. [13] The speed and relatively good accuracy of BLAST are among the key technical innovations of the BLAST programs. An overview of the BLAST algorithm (a protein to protein search) is as follows: [13]
A more complete list of available software categorized by algorithm and alignment type is available at sequence alignment software, but common software tools used for general sequence alignment tasks include ClustalW2 [45] and T-coffee [46] for alignment, and BLAST [47] and FASTA3x [48] for database searching.
BLAST (biotechnology), Basic Local Alignment Search Tool, an algorithm used in bioinformatics; Blast cell or precursor cell, in cytology, a type of partially differentiated, usually unipotent cell; Blast disease, a disease of cereal crops; Blast injury, a complex type of physical trauma resulting from direct or indirect exposure to an explosion
The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases.
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. [1]
First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. Generated with ClustalX.. Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
The algorithm starts with a completely unresolved tree, whose topology corresponds to that of a star network, and iterates over the following steps, until the tree is completely resolved, and all branch lengths are known: Based on the current distance matrix, calculate a matrix (defined below).
Hirschberg's algorithm is a generally applicable algorithm for optimal sequence alignment. BLAST and FASTA are suboptimal heuristics.If and are strings, where = and =, the Needleman–Wunsch algorithm finds an optimal alignment in () time, using () space.