, Volume 1, Issue 1, pp 9-28
Date: 13 Oct 2012

Genome data classification based on fuzzy matching

Abstract

Genomic data mining and knowledge extraction is an important problem in bioinformatics. Some research work has been done on unknown genome identification and is based on exact pattern matching of n-grams. In most of the real world biological problems exact matching may not give desired results and the problem in using n-grams is exponential explosion. In this paper we propose a method for genome data classification based on approximate matching. The algorithm works by selecting random samples from the genome database. Tolerance is allowed by generating candidates of varied length to query from these sample sequences. The Levenshtein distance is then checked for each candidate and whether they are k-fuzzily equal. The total number of fuzzy matches for each sequence is then calculated. This is then classified using the data mining techniques namely, naive Bayes, support vector machine, back propagation and also by nearest neighbor. Experiment results are provided for different tolerance levels and they show that accuracy increases as tolerance does. We also show the effect of sampling size on the classification accuracy and it was observed that classification accuracy increases with sampling size. Genome data of two species namely Yeast and E. coli are used to verify proposed method.