BLAST - Revision history

Leandra at 10:40, 22 June 2007

2007-06-22T10:40:37Z

←Older revision		Revision as of 10:40, 22 June 2007
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-	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.	+	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.
-		+
-	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.	+

	===How to reach and use BLAST===		===How to reach and use BLAST===
	:BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .		:BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .
-	:BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it ~~Bioinfo~~ website] through the [[PROGsDB]].	+	:BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]].
	:BLAST can be also launched by [[CAPRI]].		:BLAST can be also launched by [[CAPRI]].

Line 30:		Line 28:
	===References===		===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.		: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 ~~more~~ details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]	+	: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}}		{{footer\|footername=footer bioinfo}}

Giovanni at 06:46, 22 June 2007

2007-06-22T06:46:56Z

←Older revision		Revision as of 06:46, 22 June 2007
Line 32:		Line 32:
	:For more details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]		:For more details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]

-	{{footer bioinfo}}	+	{{footer\|footername=footer bioinfo}}

Giovanni at 15:50, 20 June 2007

2007-06-20T15:50:09Z

←Older revision		Revision as of 15:50, 20 June 2007
Line 31:		Line 31:
	: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.		: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 more details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]		:For more details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]
		+
		+	{{footer bioinfo}}

Mauro at 11:24, 20 June 2007

2007-06-20T11:24:12Z

←Older revision		Revision as of 11:24, 20 June 2007
Line 16:		Line 16:
	:*'''blastn''' : compares a nucleotide query sequence against a nucleotide 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		:*'''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	+	:*'''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.

Mauro at 11:23, 20 June 2007

2007-06-20T11:23:52Z

←Older revision		Revision as of 11:23, 20 June 2007
Line 3:		Line 3:
	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.		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.

-	===How to reach BLAST===	+	===How to reach and use BLAST===
-	BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .	+	:BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .
-	BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].	+	:BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].
-	BLAST can be also launched by [[CAPRI]].	+	: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''.	+	: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''.

	===Available Programs===		===Available Programs===
-	'''[http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php Blastall]''' is probably the most famous utility and includes a family of algorithms, such as:	+	:'''[http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php 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
-	*'''blastn''' : compares a nucleotide query sequence against a nucleotide 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	+	:*'''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	+	.*'''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>~~	+
-	~~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~~]	+	: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 more details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]	+	===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 more details about NCBI BLAST, visit the [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs BLAST web site]

Mauro at 10:50, 20 June 2007

2007-06-20T10:50:51Z

←Older revision		Revision as of 10:50, 20 June 2007
Line 22:		Line 22:
	*'''[http://bioinfo.ceinge.unina.it/tools/winterf/bl2seq.php bl2seq]''' : compares two sequences using one of the same blastall algorithms described above;		*'''[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:		*'''Blastpgp''' : perform ''iterative searches'', in two different modes:
-	**''[http://bioinfo.ceinge.unina.it/tools/winterf/~~bl2seq~~.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/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.		**''[http://bioinfo.ceinge.unina.it/tools/winterf/phiblast.php phi-blast]'' : combines matching of regular expressions with local alignments surrounding each identified match.

Mauro at 10:50, 20 June 2007

2007-06-20T10:50:13Z

←Older revision		Revision as of 10:50, 20 June 2007
Line 23:		Line 23:
	*'''Blastpgp''' : perform ''iterative searches'', in two different modes:		*'''Blastpgp''' : perform ''iterative searches'', in two different modes:
	**''[http://bioinfo.ceinge.unina.it/tools/winterf/bl2seq.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/bl2seq.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.	+	**''[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]		A more detailed description of each BLAST utility available [http://bioinfo.ceinge.unina.it/help/blast/ here]

Mauro at 10:49, 20 June 2007

2007-06-20T10:49:38Z

Mauro at 10:46, 20 June 2007

2007-06-20T10:46:06Z

←Older revision		Revision as of 10:46, 20 June 2007
Line 1:		Line 1:
	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.		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.

-	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 the ~~speed-up~~ of the cluster.	+	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 the high computer resources of the cluster.

	=== How to reach BLAST ===		=== How to reach BLAST ===

Mauro at 10:44, 20 June 2007

2007-06-20T10:44:47Z

←Older revision		Revision as of 10:44, 20 June 2007
Line 1:		Line 1:
	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.		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.

-	The NCBI BLAST (version 2.2.12) is installed on the [[cluster]] ~~machine~~, 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.	+	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 the speed-up of the cluster.

	=== How to reach BLAST ===		=== How to reach BLAST ===

←Older revision		Revision as of 10:49, 20 June 2007
Line 1:		Line 1:
	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.		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.

-	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 ~~the high~~ computer resources of the cluster.	+	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.

-	=== How to reach BLAST ===	+	===How to reach BLAST===
	BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .		BLAST can be launched by clicking [http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php here] .
	BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].		BLAST utilities can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].
Line 11:		Line 11:

	===Available Programs===		===Available Programs===
-	'''Blastall''' is probably the most famous utility and includes a family of algorithms, such as:	+	'''[http://bioinfo.ceinge.unina.it/tools/winterf/blast2.php 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
Line 20:		Line 20:
	<br>		<br>
	Other advanced utilities are also available:		Other advanced utilities are also available:
-	*'''bl2seq''' : compares two sequences using one of the same blastall algorithms described above;	+	*'''[http://bioinfo.ceinge.unina.it/tools/winterf/bl2seq.php 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:		*'''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.	+	**''[http://bioinfo.ceinge.unina.it/tools/winterf/bl2seq.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.
-	**''phi-blast'' : combines matching of regular expressions with local alignments surrounding each identified match.	+	**''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]		A more detailed description of each BLAST utility available [http://bioinfo.ceinge.unina.it/help/blast/ here]