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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. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query ...
BLAST, on the other hand, builds an index of the query sequences and searches through the database for matches. [1] 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 ...
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each node. [2] Protein: Burdyshaw CE, Sawyer S, Horton MD, Brook RG, Rekapalli B: 2017 CS-BLAST: Sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH.
A Gap penalty is a method of scoring alignments of two or more sequences. When aligning sequences, introducing gaps in the sequences can allow an alignment algorithm to match more terms than a gap-less alignment can. However, minimizing gaps in an alignment is important to create a useful alignment.
One PAM unit is defined as 1% of the amino acid positions that have been changed. To create a PAM1 substitution matrix, a group of very closely related sequences with mutation frequencies corresponding to one PAM unit is chosen. Based on collected mutational data from this group of sequences, a substitution matrix can be derived.
CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. PSI-BLAST (Position-Specific Iterated BLAST) runs at about the same speed per iteration as regular BLAST, but is able to detect weaker sequence similarities that are still ...
Here, is the probability of two amino acids and replacing each other in a homologous sequence, and and are the background probabilities of finding the amino acids and in any protein sequence. The factor λ {\displaystyle \lambda } is a scaling factor, set such that the matrix contains easily computable integer values.