BLAST
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| === How to reach and use BLAST === | === How to reach and use BLAST === | ||
| BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[searchable programs interface]]. | BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[searchable programs interface]]. | ||
| - | + | BLASTALL can be also launched by [[CAPRI]]. | |
| - | + | ||
| In the [[VLS]] environment, the BLAST package is fully available for command line use in the directory ''/bioprogs/blast''. The blastable libraries are located in the directory ''/biodata/dbs/blast''. | In the [[VLS]] environment, the BLAST package is fully available for command line use in the directory ''/bioprogs/blast''. The blastable libraries are located in the directory ''/biodata/dbs/blast''. | ||
Revision as of 20:07, 11 June 2007
Contents |
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 programs can be run by the command-line utilities.
Blastall is probably the most famous utility and 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 advanced 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 : 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 each identified match.
A more detailed description of each BLAST utility available here
BLAST at CEINGE
At CEINGE the NCBI BLAST is installed on the cluster machine, together with the most famous sequence libraries (such as EMBL, UNIPROT, ENSEMBL), which are automatically updated every night. The local installation of BLAST and relative libraries allows to customize and speed up sequence analysis in different group research projects, such as in automatic annotation systems.
How to reach and use BLAST
BLAST utilities can be searched and launched from the Bioinfo website through the searchable programs interface. BLASTALL can be also launched by CAPRI.
In the VLS environment, the BLAST package is fully available for command line use in the directory /bioprogs/blast. The blastable libraries are located in the directory /biodata/dbs/blast.
