Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

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.

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Francis C. Weng, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Huai-Kuang Tsai, Daryi Wang
• Keywords: BMCBI 2010, Taxonomic Binning, Taxonomic Binning Tools, Uncultured Microbial Communities