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
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 ...
Toward a standard in structural genome annotation for prokaryotes
Standards in Genomic Sciences - Tập 10 - Trang 1-9 - 2015
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...
Complete genome sequence of Pyrobaculum oguniense
Standards in Genomic Sciences - Tập 6 - Trang 336-345 - 2012
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...
Complete genome sequence of Gordonia bronchialis type strain (3410T)
Standards in Genomic Sciences - Tập 2 - Trang 19-28 - 2010
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...
Genome sequence and description of Corynebacterium ihumii sp. nov.
Standards in Genomic Sciences - Tập 9 - Trang 1128-1143 - 2014
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...
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
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...
Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis strain LM 4–2
Standards in Genomic Sciences - Tập 10 - Trang 1-7 - 2015
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 chromosome with
average GC cont...
Complete genome sequence of Roseophage vB_DshP-R1, which infects Dinoroseobacter shibae DFL12
Standards in Genomic Sciences -
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
Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3
Standards in Genomic Sciences - Tập 10 - Trang 1-8 - 2015
Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate
oxidizing bacterium, belonging to the Clostridia class within the phylum
Firmicutes, originally isolated from a mesophilic methanogenic digester. It has
been shown to oxidize acetate in co-cultivation with hydrogenotrophic
methanogens forming methane. The draft genome shows a total size of
3,196,921 bp, encoding 3,688 open rea...
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