A novel hierarchical clustering algorithm for gene sequences.

ABSTRACT:

Background

Clustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. This method transforms DNA sequences into the feature vectors which contain the occurrence, location and order relation of k-tuples in DNA sequence. Afterwards, a hierarchical procedure is applied to clustering DNA sequences based on the feature vectors.

Results

The proposed distance measure and clustering method are evaluated by clustering functionally related genes and by phylogenetic analysis. This method is also compared with BlastClust, CD-HIT-EST and some others. The experimental results show our method is effective in classifying DNA sequences with sim

SUBMITTER: Wei D 

PROVIDER: S-EPMC3443659 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature