Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency |
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Authors: | Francis C Weng Chien-Hao Su Ming-Tsung Hsu Tse-Yi Wang Huai-Kuang Tsai Daryi Wang |
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Affiliation: | 1.Biodiversity Research Center,Academia Sinica,Taipei,Taiwan;2.Institute of Information Science,Academia Sinica,Taipei,Taiwan;3.Research Center for Information Technology Innovation,Academia Sinica,Taipei,Taiwan;4.Department of Computer Science and Information Engineering,National Taiwan University,Taipei,Taiwan |
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Abstract: | Background Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies. |
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