Standards in Genomic Sciences

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Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard
Standards in Genomic Sciences - - 2011
Melissa Beth Duhaime, Renzo Kottmann, Dawn Field, Frank Oliver Glöckner
In any sequencing project, the possible depth of comparative analysis is determined largely by the amount and quality of the accompanying contextual data. The structure, content, and storage of this contextual data should be standardized to ensure consistent coverage of all sequenced entities and facilitate comparisons. The Genomic Standards Consortium (GSC) has developed the “Minimum Information ...... hiện toàn bộ
Toward a standard in structural genome annotation for prokaryotes
Standards in Genomic Sciences - Tập 10 - Trang 1-9 - 2015
H. James Tripp, Granger Sutton, Owen White, Jennifer Wortman, Amrita Pati, Natalia Mikhailova, Galina Ovchinnikova, Samuel H. Payne, Nikos C. Kyrpides, Natalia Ivanova
In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, 1,004,576 peptides were collected from various publicly available resources, and were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an average GC content from 31 % to 74 %, biased toward h...... hiện toàn bộ
Complete genome sequence of Pyrobaculum oguniense
Standards in Genomic Sciences - Tập 6 - Trang 336-345 - 2012
David L. Bernick, Kevin Karplus, Lauren M. Lui, Joanna K. C. Coker, Julie N. Murphy, Patricia P. Chan, Aaron E. Cozen, Todd M. Lowe
Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot spring in Japan. Here we describe its main chromosome of 2,436,033 bp, with three large-scale inversions and an extra-chromosomal element of 16,887 bp. We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome, including nine H/ACA-like small RNA, 83 predicted C/D box small RNA, and 47 tr...... hiện toàn bộ
Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert
Standards in Genomic Sciences - Tập 9 - Trang 304-314 - 2013
Nisha Tak, Hukam S. Gehlot, Muskan Kaushik, Sunil Choudhary, Ravi Tiwari, Rui Tian, Yvette Hill, Lambert Bräu, Lynne Goodwin, James Han, Konstantinos Liolios, Marcel Huntemann, Krishna Palaniappan, Amrita Pati, Konstantinos Mavromatis, Natalia Ivanova, Victor Markowitz, Tanja Woyke, Nikos Kyrpides, Wayne Reeve
Ensifer sp. TW10 is a novel N2-fixing bacterium isolated from a root nodule of the perennial legume Tephrosia wallichii Graham (known locally as Biyani) found in the Great Indian (or Thar) desert, a large arid region in the northwestern part of the Indian subcontinent. Strain TW10 is a Gram-negative, rod shaped, aerobic, motile, non-spore forming, species of root nodule bacteria (RNB) that promisc...... hiện toàn bộ
Complete genome sequence of Gordonia bronchialis type strain (3410T)
Standards in Genomic Sciences - Tập 2 - Trang 19-28 - 2010
Natalia Ivanova, Johannes Sikorski, Marlen Jando, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, Cliff Han, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, Nikos C. Kyrpides
Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944...... hiện toàn bộ
Genome sequence and description of Corynebacterium ihumii sp. nov.
Standards in Genomic Sciences - Tập 9 - Trang 1128-1143 - 2014
Roshan Padmanabhan, Grégory Dubourg, Jean-Christophe Lagier, Carine Couderc, Caroline Michelle, Didier Raoult, Pierre-Edouard Fournier
Corynebacterium ihumii strain GD7T sp. nov. is proposed as the type strain of a new species, which belongs to the family Corynebacteriaceae of the class Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old male patient, as a part of the culturomics study. _Corynebacterium ihumii is a Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe the fea...... hiện toàn bộ
Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens and plant growth promoting abilities
Standards in Genomic Sciences - Tập 11 - Trang 1-8 - 2016
Eveline Adam, Henry Müller, Armin Erlacher, Gabriele Berg
The Serratia plymuthica strains 3Rp8 and 3Re4-18 are motile, Gram-negative, non-sporulating bacteria. Strain 3Rp8 was isolated from the rhizosphere of Brassica napus L. and strain 3Re4-18 from the endorhiza of Solanum tuberosum L. Studies have shown in vitro activity against the soil-borne fungi Verticillium dahliae Kleb., Rhizoctonia solani Kühn, and Sclerotinia sclerotiorum. Here, we announce an...... hiện toàn bộ
Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis strain LM 4–2
Standards in Genomic Sciences - Tập 10 - Trang 1-7 - 2015
Xiao-Yan You, Hui Wang, Guang-Yue Ren, Jing-Jing Li, Xu Duan, Hua-Jun Zheng, Zheng-Qiang Jiang
Bacillus subtilis LM 4–2, a Gram-positive bacterium was isolated from a molybdenum mine in Luoyang city. Due to its strong resistance to molybdate and potential utilization in bioremediation of molybdate-polluted area, we describe the features of this organism, as well as its complete genome sequence and annotation. The genome was composed of a circular 4,069,266 bp chromo...... hiện toàn bộ
Complete genome sequence of Roseophage vB_DshP-R1, which infects Dinoroseobacter shibae DFL12
Standards in Genomic Sciences -
Jianda Ji, Rui Zhang, Nianzhi Jiao
Genomic analysis of Agrobacterium radiobacter DSM 30147T and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993
Standards in Genomic Sciences - Tập 9 Số 3 - Trang 574-584
Lin-Shuang Zhang, Xiangyang Li, Feng Zhang, Gejiao Wang
Tổng số: 547   
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