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Comprehensive Microbial Resource specifications

Information


Unique identifier OMICS_20989
Name Comprehensive Microbial Resource
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

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Publications for Comprehensive Microbial Resource

Comprehensive Microbial Resource citations

 (44)
call_split

Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history

2018
BMC Genomics
PMCID: 5789663
PMID: 29378510
DOI: 10.1186/s12864-018-4487-2
call_split See protocol

[…] oundings regions) and detection of putative operons. The clustering of regulated genes into functional groups was performed using the Bioprocess classification in MicroScope [], which is based on the Comprehensive Microbial Resource (CMR, http://cmr.jcvi.org) []. […]

library_books

Comparative Genomic Analysis Reveals Habitat Specific Genes and Regulatory Hubs within the Genus Novosphingobium

2017
mSystems
PMCID: 5443232
PMID: 28567447
DOI: 10.1128/mSystems.00020-17

[…] enes in the orthologs was identified using the Database of Essential Genes (DEG) version 13.3 (). The genome completeness was estimated by analyzing the presence of 107 essential copy genes using the Comprehensive Microbial Resource as a database, where 107 hidden Markov models (HMMs) of essential copy genes were analyzed in all of the Novosphingobium strains (). […]

library_books

A novel small RNA CoaR regulates coenzyme A biosynthesis and tolerance of Synechocystis sp. PCC6803 to 1 butanol possibly via promoter directed transcriptional silencing

2017
Biotechnol Biofuels
PMCID: 5319066
PMID: 28239414
DOI: 10.1186/s13068-017-0727-y

[…] coverer software (Version 1.2.0.208) (Thermo Scientific) with default parameters to generating peak list. Genome sequence and annotation information of Synechocystis were downloaded from NCBI and the Comprehensive Microbial Resource (CMR) of TIGR (http://www.tigr.org/CMR) []. Proteins with 1.2-fold change between the CoaR(+) strain and control WT samples and p-value of statistical evaluation <0.05 […]

library_books

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India

2015
BMC Microbiol
PMCID: 4619388
PMID: 26498929
DOI: 10.1186/s12866-015-0574-6

[…] ] with the bacterial codon table (gyrA: reading frame 1, parC: reading frame 2). To remove reads from untargeted genera, all sequences annotated with gene symbol gyrA or parC were downloaded from the Comprehensive Microbial Resource (CMR) [] and matched to all reads using BLASTn []. Only reads with their best hit to Escherichia or Shigella and with E-values less than 1 × 10−100 were used in this s […]

call_split

Comparative analyses of proteins from Haemophilus influenzae biofilm and planktonic populations using metabolic labeling and mass spectrometry

2014
BMC Microbiol
PMCID: 4302520
PMID: 25551439
DOI: 10.1186/s12866-014-0329-9
call_split See protocol

[…] e differentially expressed proteins, a fold-change threshold was not applied to the data. Predicted protein roles were determined using the role identification tool from the J. Craig Venter Institute Comprehensive Microbial Resource website (http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi) []. In a few cases this search generated a predicted protein role as “unknown”. These proteins were further i […]

library_books

Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen

2014
MBio
PMCID: 4173771
PMID: 25161187
DOI: 10.1128/mBio.01045-13

[…] 2 (CD2975), cas1 (CD2976), cas4 (CD2977), cas3 (CD2978), cas5 (CD2979), cas7 (or cst2) (CD2980), cas8b (or cst1) (CD2981), and cas6 (CD2982), as assigned by the Genome Properties Report from the JCVI Comprehensive Microbial Resource. These genes are near to the largest of the CD630 CRISPR arrays, NC_009089_17, which contains 19 spacers. The second set of predicted cas genes is distinct from the de […]

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Comprehensive Microbial Resource institution(s)
J. Craig Venter Institute, Rockville, MD, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
Comprehensive Microbial Resource funding source(s)
Supported by Department of Energy [DE-FC02-95ER61962, DE-FG02- 01ER63203]; and the National Science Foundation [DBI- 0110270].

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