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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 ...
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.
BLAT can be used for alignments of two protein sequences. However, it is not the tool of choice for these types of alignments. BLASTP, the Standard Protein BLAST tool, is more efficient at protein-protein alignments; [1] Determination of the distribution of exonic and intronic regions of a gene; [9] [10]
The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature.
Alignments for membrane protein sequences: Protein: Both: M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest: 2013 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017
One would use a higher numbered BLOSUM matrix for aligning two closely related sequences and a lower number for more divergent sequences. It turns out that the BLOSUM62 matrix does an excellent job detecting similarities in distant sequences, and this is the matrix used by default in most recent alignment applications such as BLAST .
PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. Users send a protein sequence and receive a single file with results from database comparisons and prediction methods.
PIR was established in 1984 by the National Biomedical Research Foundation as a resource to assist researchers and customers in the identification and interpretation of protein sequence information. Prior to that, the foundation compiled the first comprehensive collection of macromolecular sequences in the Atlas of Protein Sequence and ...