Genomics Inform.  2012 Mar;10(1):44-50. 10.5808/GI.2012.10.1.44.

Efficient Mining of Interesting Patterns in Large Biological Sequences

• Rashid MM
• Karim MR
• Jeong BS
• Choi HJ

• KMID: 2053284
• DOI: http://doi.org/10.5808/GI.2012.10.1.44

Abstract

Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time.

Keyword

DNA sequence; index-based method; information gain; pattern mining

MeSH Terms

Base Sequence
Computational Biology
DNA
Mining
DNA