BLAST

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	===Overview===		===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.	+	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.
	There are essentialy two different implementation of the BLAST algorithm: NCBI BLAST an WU-BLAST, developed at NCBI and Washington University, respectively.		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.		At CEINGE the NCBI BLAST is installed.
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	===Programs===		===Programs===
	The NCBI BLAST family of programs includes:		The NCBI BLAST family of programs includes:

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Revision as of 19:29, 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 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. 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.