Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)

Standards in Genomic Sciences - Tập 4 Số 1 - Trang 45-53
Amrita Pati1, Sabine Gronow2, Ahmet Zeytun3, Alla Lapidus1, Matt Nolan1, Nancy Hammon, Shweta Deshpande1, Jan‐Fang Cheng1, Roxane Tapia3, Cliff Han3, Lynne Goodwin3, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen4, Krishna Palaniappan4, Miriam Land5, Loren Hauser5, Yun Juan Chang5, Cynthia D. Jeffries5, John C. Detter1, Evelyne Brambilla2, Manfred Rohde6, Markus Göker2, Tanja Woyke1, James Bristow, Jonathan A. Eisen7, Victor Markowitz4, Philip Hugenholtz8, Nikos C. Kyrpides1, Hans Peter Klenk2, Susan Lucas1,9,10,11,12,13,14
11DOE Joint Genome Institute, Walnut Creek, California, USA
22DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
33Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
44Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
55Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
66HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
77University of California Davis Genome Center, Davis, California, USA
88Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
9Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
10Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
11DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
12Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
13Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
14University of California Davis Genome Center, Davis, California, USA

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Tài liệu tham khảo

Garrity, 2010, NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser., Microbiol Today, 7, 1

Benno, 1983, Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., new species from abscesses and feces of pigs., Syst Appl Microbiol, 4, 396, 10.1016/S0723-2020(83)80024-1

DeSantis, 2006, Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB., Appl Environ Microbiol, 72, 5069, 10.1128/AEM.03006-05

Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.

Yarza, 2008, The all-species living tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains., Syst Appl Microbiol, 31, 241, 10.1016/j.syapm.2008.07.001

Lee, 2002, Multiple sequence alignment using partial order graphs., Bioinformatics, 18, 452, 10.1093/bioinformatics/18.3.452

Castresana, 2000, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis., Mol Biol Evol, 17, 540, 10.1093/oxfordjournals.molbev.a026334

Stamatakis, 2008, A rapid bootstrap algorithm for the RAxML web-servers., Syst Biol, 57, 758, 10.1080/10635150802429642

Pattengale, 2009, How Many Bootstrap Replicates Are Necessary?, Lect Notes Comput Sci, 5541, 184, 10.1007/978-3-642-02008-7_13

Liolios, 2010, The Genomes OnLine Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata., Nucleic Acids Res, 38, D346, 10.1093/nar/gkp848

Cerdeño-Tárraga, 2005, Extensive DNA inversions in the B. fragilis genome control variable gene expression., Science, 307, 1463, 10.1126/science.1107008

Field, 2008, The minimum information about a genome sequence (MIGS) specification., Nat Biotechnol, 26, 541, 10.1038/nbt1360

Woese, 1990, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya., Proc Natl Acad Sci USA, 87, 4576, 10.1073/pnas.87.12.4576

Ludwig W, Euzeby J, Whitman WG. Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Taxonomic Outline 2008.

Skerman, 1980, Approved Lists of Bacterial Names., Int J Syst Bacteriol, 30, 225, 10.1099/00207713-30-1-225

Cato, 1982, Bacteroides zoogleoformans, Weinberg, Nativelle, and Prévot 1937) corrig. comb. nov.: emended description., Int J Syst Bacteriol, 32, 271, 10.1099/00207713-32-3-271

Shah, 1989, Proposal to restrict the genus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and closely related species., Int J Syst Bacteriol, 39, 85, 10.1099/00207713-39-1-85

1983, Validation List no. 12. Validation of the publication of new names and new combinations previously effectively published outside the IJSB., Int J Syst Bacteriol, 33, 896, 10.1099/00207713-33-4-896

Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 466.

Ashburner, 2000, Gene Ontology: tool for the unification of biology., Nat Genet, 25, 25, 10.1038/75556

Saito, 1963, Preparation of transfroming deoxyribonucleic acid by phenol treatment., Biochim Biophys Acta, 72, 619, 10.1016/0926-6550(63)90386-4

Klenk, 2010, En route to a genome-based classification of Archaea and Bacteria?, Syst Appl Microbiol, 33, 175, 10.1016/j.syapm.2010.03.003

Wu, 2009, A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea., Nature, 462, 1056, 10.1038/nature08656

List of growth media used at DSMZ: http//www.dsmz.de/microorganisms/media_list.php.

Gemeinholzer, The DNA Bank Network: the start from a German initiative., Biopreservation and Biobanking.

DNA Bank Network. www.dnabank-network.org

DOE Joint Genome Institute. http://www.jgi.doe.gov/

Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com

Zerbino, 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs., Genome Res, 18, 821, 10.1101/gr.074492.107

Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification., BMC Bioinformatics, 11, 119, 10.1186/1471-2105-11-119

Pati, 2010, GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes., Nat Methods, 7, 455, 10.1038/nmeth.1457

Markowitz, 2009, IMG ER: a system for microbial genome annotation expert review and curation., Bioinformatics, 25, 2271, 10.1093/bioinformatics/btp393

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Standards in Genomic Sciences

Tập 4 Số 1

45-53

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