Journal article

Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing

Chon-Kit Kenneth Chan, Arthur L Hsu, Sen-Lin Tang, Saman K Halgamuge

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY | HINDAWI LTD | Published : 2008

Abstract

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..

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University of Melbourne Researchers