BLAST

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	==BLAST==		==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.	+	===Overview===
		+	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.
		+	There are essentialy 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 NCBI BLAST family of programs includes:
-	BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs.	+	*'''blastp''': compares an amino acid query sequence against a protein sequence database
-	There are aminly two different implementation of BLAST: NCBI BLAST an WU-BLAST, developed at NCBI and Washington University, respectively.	+	*'''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.
-	At CEINGE the NCBI BLAST is installed. The NCBI BLAST family of programs includes:	+	<br><br>
		+	For a more detailed description of the t
-	{| border="1" cellspacing="0" cellpadding="5" align="left"	+	===BLAST at CEINGE===
-	! Program	+	At CEINGE the NCBI BLAST is installed on the [[cluster]] machine.
-	! description	+
-	|-	+
-	| '''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.	+
-	|-	+
-	|}	+

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Revision as of 19:28, 11 June 2007

Contents 1 BLAST 1.1 Overview 1.2 Programs 1.3 BLAST at CEINGE

BLAST

Overview

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. There are essentialy 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 NCBI BLAST family of programs includes:

• 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.

For a more detailed description of the t

BLAST at CEINGE

At CEINGE the NCBI BLAST is installed on the cluster machine.