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joint_genomics specifications

Information


Unique identifier OMICS_09004
Name joint_genomics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Lingling Zheng <>

Publication for joint_genomics

joint_genomics in publications

 (11)
PMCID: 5422444
PMID: 28536564
DOI: 10.3389/fmicb.2017.00809

[…] of this research theme, and they must be better understood and adequately addressed for more genomes of these microorganisms to become available. this review explores these factors and highlights joint genomics/metagenomics workflows that aim to overcome some of the challenges commonly found in cyanobacteriology., in 1996, synechocystis sp. pcc 6803 became the first cyanobacterium […]

PMCID: 5054325
PMID: 27795254
DOI: 10.1128/genomeA.01086-16

[…] an accuracy of >99.999%. the final assembly was a single, circular chromosome comprising 3,243,537 bp with an average coverage of 467×. the genome was annotated by both the department of energy’s joint genomics institute integrated microbial genomes (jgi-img) system and the ncbi prokaryotic genome annotation pipeline. the jgi-img annotation predicted 3,114 genes, of which 3,053 were predicted […]

PMCID: 4956451
PMID: 27445378
DOI: 10.1128/genomeA.00686-16

[…] of 68.6%., gene prediction analysis and functional annotations were performed within the integrated microbial genomes-expert review (img-er) platform (http://img.jgi.doe.gov) developed by the joint genomics institute (jgi) (), using the department of energy (doe)-jgi microbial genome annotation pipeline. a total of 3,832 genes were predicted, including 3,757 coding sequence (cds) […]

PMCID: 4498109
PMID: 26159523
DOI: 10.1128/genomeA.00700-15

[…] were predicted with trnascan-se 1.23 () and rrnas were predicted with rnammer 1.2 (). the kegg pathways and pfam annotation were analyzed using webmga (). the annotated genome was submitted to the joint genomics institute (img/er database) (https://img.jgi.doe.gov/cgi-bin/er/main.cgi) which was used to refine the annotation and registration at the international nucleotide sequence database […]

PMCID: 4424285
PMID: 25953169
DOI: 10.1128/genomeA.00287-15

[…] contaminant, we used mummer () to align the assembled draft genome to the genomes of a previously sequenced t. atroviride strain (imi206040) () and a t. harzianum strain (cbs226.95) available at the joint genomics institute (jgi) (http://genome.jgi.doe.gov/triha1/). the alignment showed that 92% of the t. atroviride genome aligns to 83% of our genome assembly, with 99.29% identity on average, […]


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joint_genomics institution(s)
G.S.Sanyal School of Telecommunications, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India; Computational Biology & Bioinformatics, Duke University, Durham, NC, USA; Quintiles, Durham, NC, USA; Electrical & Computer Engineering Department, Duke University, Durham, NC, USA
joint_genomics funding source(s)
This work was supported in part by Biomedical Advanced Research and Development Authority (BARDA) and the Office of Naval Research.

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