BLAST
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| ===Programs=== | ===Programs=== | ||
| - | The BLAST programs can be run by the command-line utilities. <br>'''Blastall''' is probably the most famous | + | The BLAST programs can be run by the command-line utilities. <br>'''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 | *'''blastp''': compares an amino acid query sequence against a protein sequence database | ||
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| *'''tblastn''': compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames | *'''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. | *'''tblastx''': compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. | ||
| - | <br> | + | <br><br> |
| - | Other | + | Other advanced utilities are also available: |
| *'''bl2seq''': compares two sequences using one of the same blastall algorithms described above; | *'''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; | *'''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: | + | *'''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. | **''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'': | + | **''phi-blast'': combines matching of regular expressions with local alignments surrounding each identified match. |
| - | + | A more detailed description of each BLAST utility available [http://bioinfo.ceinge.unina.it/help/blast/ here] | |
| - | + | ||
| - | + | ||
| ===BLAST at CEINGE=== | ===BLAST at CEINGE=== | ||
| At CEINGE the NCBI BLAST is installed on the [[cluster]] machine. | At CEINGE the NCBI BLAST is installed on the [[cluster]] machine. | ||
Revision as of 19:50, 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: 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 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.
