M-pick, a modularity-based method for OTU picking of 16S rRNA sequences
1 Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, 32610, Gainesville, FL, USA
2 Department of Electrical and Computer Engineering, University of Florida, 32610, Gainesville, FL, USA
3 Department of Microbiology and Immunology, Center of Excellence in Bioinformatics & Life Sciences, Department of Computer Science and Engineering, The State University of New York at Buffalo, 14214, Buffalo, NY, USA
BMC Bioinformatics 2013, 14:43 doi:10.1186/1471-2105-14-43Published: 7 February 2013
Binning 16S rRNA sequences into operational taxonomic units (OTUs) is an initial crucial step in analyzing large sequence datasets generated to determine microbial community compositions in various environments including that of the human gut. Various methods have been developed, but most suffer from either inaccuracies or from being unable to handle millions of sequences generated in current studies. Furthermore, existing binning methods usually require a priori decisions regarding binning parameters such as a distance level for defining an OTU.
We present a novel modularity-based approach (M-pick) to address the aforementioned problems. The new method utilizes ideas from community detection in graphs, where sequences are viewed as vertices on a weighted graph, each pair of sequences is connected by an imaginary edge, and the similarity of a pair of sequences represents the weight of the edge. M-pick first generates a graph based on pairwise sequence distances and then applies a modularity-based community detection technique on the graph to generate OTUs to capture the community structures in sequence data. To compare the performance of M-pick with that of existing methods, specifically CROP and ESPRIT-Tree, sequence data from different hypervariable regions of 16S rRNA were used and binning results were compared.
A new modularity-based clustering method for OTU picking of 16S rRNA sequences is developed in this study. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance levels to define OTUs. The source code is available at http://plaza.ufl.edu/xywang/Mpick.htm webcite.