BLAST
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BLAST
Overview
BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing biological sequences, such as amino-acid sequences or nucleotides sequences. Through a BLAST search a researcher can compare a query sequence with a library (database) of sequences, and identify library sequences that are similar to the query sequence above a certain threshold. Essentially there are two different implementation of the BLAST algorithm: NCBI BLAST an WU-BLAST, developed at NCBI and Washington University, respectively. At CEINGE the NCBI BLAST is installed.
Programs
The BLAST program can be run by the command-line utility "blastall". Blastall includes a family of algorithms, such as:
- blastp: compares an amino acid query sequence against a protein sequence database
- blastn: compares a nucleotide query sequence against a nucleotide sequence database
- blastx: compares a nucleotide query sequence translated in all reading frames against a protein sequence database
- tblastn: compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
- tblastx: compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
Other special utilities are also available:
- bl2seq: compares two sequences using one of the same blastall algorithms described above;
- megablast: compares highly similar nucleotide sequences by concatenating many input sequences together to form a large sequence before searching the BLAST database;
- Blastpgp: perform iterative searches in two different modes:
- psi-blast: do an iterative search in which sequences found in one round of searching are used to build a score model for the next round of searching.
- phi-blast: combines matching of regular expressions with local alignments surrounding the match
For a more detailed description of the t
BLAST at CEINGE
At CEINGE the NCBI BLAST is installed on the cluster machine.
