Search results
Results from the WOW.Com Content Network
blast.ncbi.nlm.nih.gov /Blast.cgi 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.
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
Search through online databases: National Center for Biotechnology Information (NCBI), Protein Data Bank (PDB), UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, DAS servers; Local and NCBI Genbank BLAST search; Open reading frame finder; Restriction enzyme finder with integrated REBASE [5] restriction enzymes list; Integrated Primer3 package [6] for PCR ...
formatdb is a discontinued software tool that was used in molecular bioinformatics to format protein or nucleotide databases for BLAST.It has been replaced by makeblastdb and the NCBI "strongly encourage[s]" [1] users to stop using formatdb.
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.
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.
A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and search one or more databases for information related to that sequence.
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 ...