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A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold.
Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services: Nucleotide, peptide: 2010 SAM Local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST: Both: Karplus K, Krogh A [15] 1999 SSEARCH Smith-Waterman search, slower but more sensitive than FASTA: Both ...
A BLAST interface is provided to allow users to search for DNA or protein sequences against the Ensembl Genomes. It can be accessed by the header, located on top of all Ensembl Genome pages, titled BLAST. The BLAST search can be configured to search against individual species or collections of species (maximum of 25).
BLAST is an algorithm used for calculating sequence similarity between biological sequences, such as nucleotide sequences of DNA and amino acid sequences of proteins. [7] BLAST is a powerful tool for finding sequences similar to the query sequence within the same organism or in different organisms.
The BLAST family of search methods provides a number of algorithms optimized for particular types of queries, such as searching for distantly related sequence matches. BLAST was developed to provide a faster alternative to FASTA without sacrificing much accuracy; like FASTA, BLAST uses a word search of length k , but evaluates only the most ...
DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. All three accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them.
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC).
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. [1] [9]