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If one is attempting to search for a proprietary sequence or simply one that is unavailable in databases available to the general public through sources such as NCBI, there is a BLAST program available for download to any computer, at no cost. This can be found at BLAST+ executables. There are also commercial programs available for purchase.
HPC-BLAST: NCBI compliant multinode and multicore BLAST wrapper. 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
The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through internet browsers or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.
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.
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.
WU-BLAST with XDF was the first BLAST suite to support indexed-retrieval of NCBI standard FASTA-format sequence identifiers (including the entire range of NCBI identifiers); the first to allow retrieval of individual sequences in part or in whole, natively, translated or reverse-complemented; and the first able to dump the entire contents of a ...
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).
NCBI-BLAST, an algorithm for comparing biological sequences from the NCBI; Ensembl, automatic gene annotation by the EMBL-EBI and Sanger Institute; FlyBase is a database of model organism Drosophila melanogaster; GoPubMed is a knowledge-based search engine for biomedical texts; iHOP, information hyperlinked over proteins via gene/protein synonyms