Metagenome Fragment Binning Based on Characterization Vectors

We propose an approach for metagenome fragment binning using support vector machine (SVM) and characterization vectors. We developed this method to overcome the limitation of the composition-based approach using k-mer features to perform the binning process, particularly for short fragments. We take advantage of characterization vectors, which consider global information of DNA fragments without performing sequence alignments. The global information of sequences can be represented by twelve-dimensional information. Our experiments show that this method is highly accurate for binning metagenome fragments at the genus level with fragment lengths > 500 bp for datasets representing known and new organisms. This approach is promising for extension to other taxonomy levels.
metagenome binning characterization vector support vector machine
Wisnu Ananta Kusuma Yutaka Akiyama
Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology Tokyo, Japan
国际会议
三亚
英文
50-54
2011-03-25(万方平台首次上网日期,不代表论文的发表时间)