Oracle Tips by Burleson

Oracle 10g Sequence Matching and Annotation (BLAST)

Oracle Database 10g helps biologists solve many problems in the field of bioinformatics.  One of the features Oracle 10g provides is Sequence Similarity Search (Sequence Alignment).  Sequence alignment is one of the most common bioinformatics tasks.  It provides a way to compare new sequences with previously characterized sequences. 

The most widely used sequence-matching tool is BLAST (Basic Local Alignment Search Tool).  The BLAST family of algorithms generates statistics on gapped and un-gapped sequence alignments.  Some of the functions Oracle 10g provides include:

• Perform a search of nucleotide sequences using the blastn_match () table function.
   

• Perform a search of protein sequences using the blastp_match () table function
   

• Perform a search with translations using the tblast_match () table function.
   

• Retrieve alignment information using blastin_align (), blastp_align (), or tblast_align () table functions.

Get the complete Oracle10g story:

The above text is an excerpt from "Oracle Database 10g New Features: Oracle10g Reference for Advanced Tuning and Administration", by Rampant TechPress.  Written by top Oracle experts, this book has a complete online code deport with ready to use scripts. 

To get the code instantly, click here:

http://rampant-books.com/book_2003_2_oracle10g.htm

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