title: An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus.
abstract: Advances in Next Generation Sequencing technologies have enabled the generation of millions of sequences from microorganisms. However, distinguishing the sequence of a novel species from sequencing errors remains a technical challenge when the novel species is highly divergent from the closest known species. To solve such a problem, we developed a new method called Optimistic Protein Assembly from Reads (OPAR). This method is based on the assumption that protein sequences could be more conserved than the nucleotide sequences encoding them. By taking advantage of metagenomics, bioinformatics and conventional Sanger sequencing, our method successfully identified all coding regions of the mouse picobirnavirus for the first time. The salvaged sequences indicated that segment 1 of this virus was more divergent from its homologues in other Picobirnaviridae species than segment 2. For this reason, only segment 2 of mouse picobirnavirus has been detected in previous studies. OPAR web tool is available at http://bioinformatics.czc.hokudai.ac.jp/opar/.
authors.affiliation: Bioinformatics Division, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Gonzalez
authors.affiliation: Department of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
authors.forename: Michihito
authors.initials: M
authors.lastname: Sasaki
authors.affiliation: UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
authors.forename: Lucy
authors.initials: L
authors.lastname: Burkitt-Gray
authors.affiliation: Immune Homeostasis Laboratory, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
authors.forename: Tomonori
authors.initials: T
authors.lastname: Kamiya
authors.affiliation: Immune Homeostasis Laboratory, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
authors.forename: Noriko M
authors.initials: NM
authors.lastname: Tsuji
authors.affiliation: Department of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.|Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.|Global Virus Network, Baltimore, MD, USA.
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Sawa
authors.affiliation: Bioinformatics Division, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
authors.forename: Kimihito
authors.initials: K
authors.lastname: Ito
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D005260:Female; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008807:Mice, Inbred BALB C; D010802:Phylogeny; D018708:Picobirnavirus / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins