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Journal of Biomedicine and Biotechnology
Volume 2008 (2008), Article ID 513701, 10 pages
Methodology Report

Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing

1Dynamic Systems & Control Group, Department of Mechanical Engineering, University of Melbourne, VIC 3010, Australia
2Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan

Received 31 August 2007; Accepted 18 November 2007

Academic Editor: Daniel Howard

Copyright © 2008 Chon-Kit Kenneth Chan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Metagenomic projects using whole-genome shotgun (WGS) sequencing produces many unassembled DNA sequences and small contigs. The step of clustering these sequences, based on biological and molecular features, is called binning. A reported strategy for binning that combines oligonucleotide frequency and self-organising maps (SOM) shows high potential. We improve this strategy by identifying suitable training features, implementing a better clustering algorithm, and defining quantitative measures for assessing results. We investigated the suitability of each of di-, tri-, tetra-, and pentanucleotide frequencies. The results show that dinucleotide frequency is not a sufficiently strong signature for binning 10 kb long DNA sequences, compared to the other three. Furthermore, we observed that increased order of oligonucleotide frequency may deteriorate the assignment result in some cases, which indicates the possible existence of optimal species-specific oligonucleotide frequency. We replaced SOM with growing self-organising map (GSOM) where comparable results are obtained while gaining speed improvement.