A Tutorial of Sequence Matching in Oracle Haifeng Ji* and Gang Qian** * Oklahoma City Community College ** University of Central Oklahoma.

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Presentation transcript:

A Tutorial of Sequence Matching in Oracle Haifeng Ji* and Gang Qian** * Oklahoma City Community College ** University of Central Oklahoma

Overview Bioinformatics requires sequence matching BLAST is one of the most widely-used tools Oracle provides a Life Science Platform that supports the BLAST functions Oracle can manage a large amount of biological data The power of SQL can be utilized to build complex queries for sequence matching The BLAST interface in Oracle can help the rapid implementation of bioinformatics applications

Introduction to BLAST BLAST has algorithms to find similarities between genome sequences (sequence homology ) Help to establish the evolutionary origin of genes Help to predict protein structures and functions BLAST is a heuristic algorithm for identifying local alignments between sequences A fast algorithm measures the statistical significance of the alignment scores with respect to a random sequence model BLAST searches both nucleotide and amino acid query sequences

Oracle BLAST Functions BLAST is implemented in Oracle Database 10g Oracle provides three MATCH functions: BLASTN_MATCH -- nucleotide sequence BLASTP_MATCH – amino acid sequences TBLAST_MATCH -- sequence involving translations

The Match Functions The MATCH functions return the information below for high scoring matches between a query sequence and a sequence database AttributeDescription t_seq_idThe identifier of the matched (target) sequence ScoreThe score of the match ValueThe expected value

SAMPLE BLAST QUERY BLASTN_MATCH() The purpose of this table function is to perform a BLASTN search of the ecoli_query sequence against the selected portion of the ecoli10 nucleotide database The database is selected using a standard SQL select and passed into the function as a reference cursor

Sample Query Select * from TABLE(BLASTN_MATCH ( (select sequence from ecoli_query), CURSOR(SELECT seq_id, seq_data FROM ecoli10)))

Query Result T_SEQ_IDSCOREEXPECT SQL>