Using Oracle Data Mining to Analyze Data

Using Oracle Data Mining to Analyze Data
Using Oracle Data Mining to Analyze Data
Purpose
This module shows you how to use Basic Local Alignment Search Tool (BLAST) to perform bioinformatics tasks.
Topics
This module will discuss the following topics:
Overview
Prerequisites
Querying Nucleotide Data
Querying Amino Acid Data
Querying Translated Data Place the cursor on this icon to display all screenshots. .
Overview
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What is BLAST?
Sequence alignment is without doubt one of the most commonly performed bioinformatics tasks. The most widely used sequence alignment algorithm is BLAST (Basic Local Alignment Search Tool). BLAST is a method for rapid sequence comparison introduced in 1990 by Stephen Altschul. It is typically used to compare a query nucleotide or amino acid sequence against a database of sequences. Its success comes from its combination of speed, sensitivity and statistical assessment of the results.
BLAST is a heuristic method to find the high scoring locally optimal alignments between a query sequence and a database. The BLAST algorithm and family of programs rely on the statistics of gapped and un-gapped sequence alignments. The statistics allow the probability of obtaining an alignment with a particular score to be estimated.
Over the last few years, as more sequence data has become available as a result of large scale sequencing efforts, BLAST has started to be used for an increasing range of sequence alignment activities which include functional annotation, gene discovery, across-organism and across-species analysis, genome assembly and completion.
Oracle10 g BLAST Functions
A version of BLAST, which is very similar to NCBI BLAST 2.0, has been implemented in the database using Table Functions. This enables users to perform BLAST queries against data that is held directly inside an Oracle database. As the algorithms are implemented as table functions, parallel computation is intrinsically supported.
The five core variants of NCBI BLAST have been implemented:
BLASTN compares a nucleotide query sequence against a nucleotide database.
BLASTN compares an amino acid query sequence against a protein sequence database.
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