BLAST

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-==BLAST==+BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing biological sequences, such as amino-acid sequences or nucleotides sequences. The NCBI BLAST (version 2.2.12) is installed on the cluster server, together with the most famous sequence libraries (such as EMBL, UNIPROT), which are automatically updated every night. The local installation of BLAST and relative libraries allow to customize and speed up sequence analysis, such as in automatic annotation of sequence projects. Having BLAST installed locally, it is also possible to create personal libraries and perform specific analyses, taking advantage from computer resources available with the cluster server.
-===Overview===+===How to reach and use BLAST===
-BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing biological sequences, such as the amino-acid sequences or the nucleotides of DNA 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.+:BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .
-There are essentialy two different implementation of the BLAST algorithm: NCBI BLAST an WU-BLAST, developed at NCBI and Washington University, respectively.+:BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]].
-At CEINGE the NCBI BLAST is installed.+:BLAST can be also launched by [[CAPRI]].
-===Programs===+
-The NCBI BLAST family of programs includes:+
-*'''blastp''': compares an amino acid query sequence against a protein sequence database+: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''.
-*'''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.+
-<br><br>+===Available Programs===
-For a more detailed description of the t+:'''[http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php Blastall]''' is probably the most famous utility and includes a family of algorithms, such as:
-===BLAST at CEINGE===+:*'''blastp''' : compares an amino acid query sequence against a protein sequence database
-At CEINGE the NCBI BLAST is installed on the [[cluster]] machine.+:*'''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:
 +:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/bl2seq.php bl2seq]''' : compares two sequences using one of the same blastall algorithms described above;
 +:*'''Blastpgp''' : perform ''iterative searches'', in two different modes:
 +:**''[http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php 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.
 +:**''[http://bioinfo.ceinge.unina.it/tools/winterf/phiblast.php 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]
 + 
 + 
 +===References===
 +:Altschul SF, Stephen F, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W and David J. Lipman DJ '''Gapped BLAST and PSI-BLAST: a new generation of protein database search programs''', ''Nucleic Acids Res.'', 1997, 25:3389-3402.
 +:For further details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]
 + 
 +{{footer|footername=footer bioinfo}}

Current revision

BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing biological sequences, such as amino-acid sequences or nucleotides sequences. The NCBI BLAST (version 2.2.12) is installed on the cluster server, together with the most famous sequence libraries (such as EMBL, UNIPROT), which are automatically updated every night. The local installation of BLAST and relative libraries allow to customize and speed up sequence analysis, such as in automatic annotation of sequence projects. Having BLAST installed locally, it is also possible to create personal libraries and perform specific analyses, taking advantage from computer resources available with the cluster server.

[edit] How to reach and use BLAST

BLAST can be launched by clicking here .
BLAST utilities can be searched and launched from the main website or through the PROGsDB.
BLAST 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.

[edit] Available Programs

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;
  • 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


[edit] References

Altschul SF, Stephen F, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W and David J. Lipman DJ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, 25:3389-3402.
For further details about NCBI BLAST, visit the BLAST web site
Bioinformatics: Bioinfo Services: Bioinfo tools: EMBOSS - PHYLIP - BLAST - SRS - ENSEMBL - CAPRI - PROGsDB
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