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Scan the database sequences for exact matches with the remaining high-scoring words. The BLAST program scans the database sequences for the remaining high-scoring word, such as PEG, of each position. If an exact match is found, this match is used to seed a possible un-gapped alignment between the query and database sequences.
The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through web 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.
Highly parallel Scalable BLAST: Both: Oehmen et al. [14] 2011 Sequilab 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
It has been replaced by makeblastdb and the NCBI "strongly encourage[s]" [1] users to stop using formatdb. formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by BLAST. [2] The source database may be in either FASTA or ASN.1 format.
The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. [1] It involves the following computerized databases : NIG 's DNA Data Bank of Japan ( Japan ), NCBI 's GenBank ( USA ) and the EMBL - EBI 's European Nucleotide Archive ( EMBL ).
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.
The NCBI team also collaborates with expert groups to develop the database and its annotation on a regular basis. Continuous evaluation of review papers and new reports of resistance proteins augment these sources. [2] While some AMR gene identification tools rely on BLAST-based methodologies, others employ hidden Markov model (HMM) approaches ...
An iframe is a window within an HTML page for an embedded view of and interactive access to the linked database. Several such iframes are combined on a single Harvester protein page. This allows simultaneous, convenient comparison of information from several databases. NCBI-BLAST, an algorithm for comparing biological sequences from the NCBI