title: Reconstructing 16S rRNA genes in metagenomic data.
abstract: Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.
  
  
  METHODS
  The source code of REAGO is freely available at https://github.com/chengyuan/reago.
authors.affiliation: Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Cheng
authors.initials: C
authors.lastname: Yuan
authors.affiliation: Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Jikai
authors.initials: J
authors.lastname: Lei
authors.affiliation: Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: James
authors.initials: J
authors.lastname: Cole
authors.affiliation: Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Yanni
authors.initials: Y
authors.lastname: Sun
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D020459:Genes, rRNA / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S