Efficient Mining of Interesting Patterns in Large Biological Sequences

• Main Authors: Md. Mamunur Rashid, Md. Rezaul Karim, Byeong-Soo Jeong, Ho-Jin Choi
• Format: Article
• Language: English
• Published: Korea Genome Organization 2012-03-01
• Series: Genomics & Informatics
• Subjects: DNA sequence; index-based method; information gain; pattern mining
• Online Access: http://genominfo.org/upload/pdf/gni-10-44.pdf

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.