Similarity evaluation of DNA sequences based on frequent patterns and entropy.

ABSTRACT:

Background

DNA sequence analysis is an important research topic in bioinformatics. Evaluating the similarity between sequences, which is crucial for sequence analysis, has attracted much research effort in the last two decades, and a dozen of algorithms and tools have been developed. These methods are based on alignment, word frequency and geometric representation respectively, each of which has its advantage and disadvantage.

Results

In this paper, for effectively computing the similarity between DNA sequences, we introduce a novel method based on frequency patterns and entropy to construct representative vectors of DNA sequences. Experiments are conducted to evaluate the proposed method, which is compared with two recently-developed alignment-free methods and the BLASTN to

SUBMITTER: Xie X 

PROVIDER: S-EPMC4331808 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature