BLASTSearch Application

BLAST (Basic Local Alignment Search Tool) Search Application uses NCBI (National Center for Biotechnology Information) BLAST technology, an algorithm for comparing biological sequence information such as nucleotide or protein sequences to a library sequence and calculates statistical match significance. It was initially developed by InforMax Inc. It is included in the Vector NTI software. The company was sold to Invitrogen in November, 2002. The basic BLAST technology has several programs.

The nucleotide blast uses a nucleotide database and includes several algorithms, which are blastn, megaBLAST and discontigouos megaBLAST. The protein blast uses a protein database and includes several algorithms, which are blastp, psi-blast, phi-blast and delta-blast. Blastx or translated BLAST compares protein sequences using a translated nucleotide query. Tblastn uses amino acid sequences and nucleotide datasets to compare protein query sequences to a nucleotide sequence. Tblastx uses a nucleotide dataset and a nucleotide sequence and compare their six-frame translations.

Blastn (nucleotide) and blastp (protein) compares nucleotide and protein sequences in FASTA format, GI number, or GenBank Accession numbers to the nucleotide and protein sequence library.  MegaBLAST perform nucleotide sequence alignment search using the GREEDY algorithm. Discontigouos megaBLAST is used for comparing diverged sequences from organisms with low degree of individuality. PSI-BLAST (Position Specific Iterative) is used to find distant protein relatives. PHI-BLAST is used for exploring protein sequences and its local alignment. DELTA-BLAST (Domain Enchanced Lookup Time Accelerated) performs searches by using a specific score matrix from an initial stored domain search