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In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
Genetic sequence alignment - In bioinformatics, gaps are used to account for genetic mutations occurring from insertions or deletions in the sequence, sometimes referred to as indels. Insertions or deletions can occur due to single mutations, unbalanced crossover in meiosis , slipped strand mispairing , and chromosomal translocation . [ 2 ]
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.
Institute of Bioinformatics (IOB), Bangalore, India: One source claims 15000 [17] proteins. But it is unclear how many of these are unique Pfam: Sanger Institute: protein families database of alignments and HMMs Protein sequence databases Human Proteinpedia: Institute of Bioinformatics (IOB), Bangalore and Johns Hopkins University,
A BLAST variant called MegaBLAST indexes 4 databases to speed up alignments. [ 9 ] BLAT can extend on multiple perfect and near-perfect matches (default is 2 perfect matches of length 11 for nucleotide searches and 3 perfect matches of length 4 for protein searches), while BLAST extends only when one or two matches occur close together.
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions ...
Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster: Protein: Steinegger M, Mirdita M, Galiez C, Söding J [10] 2017 USEARCH Ultra-fast sequence analysis tool: Both: Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics. 26 (19): 2460– 2461. doi: 10.1093/bioinformatics/btq461.
It makes use of the BLAST [5] algorithm to identify similar sequences to then transfers existing functional annotation from yet characterised sequences to the novel one. The functional information is represented via the Gene Ontology (GO), a controlled vocabulary of functional attributes.