JGI Genome Portal statistics

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Protocols

JGI Genome Portal specifications

Information


Unique identifier OMICS_29841
Name JGI Genome Portal
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 8.15.9
Maintained Yes

Maintainer


  • person_outline In Dubchak

Publication for JGI Genome Portal

JGI Genome Portal citations

 (60)
call_split

Molecular, phylogenetic and developmental analyses of Sall proteins in bilaterians

2018
PMCID: 5892016
PMID: 29644029
DOI: 10.1186/s13227-018-0096-z
call_split See protocol

[…] om Biomphalaria glabrata and C. fornicata from RNA-seq datasets generated in our lab [] and uploaded to Geneious version 6.1.2 []. Potential sequences of the snail L. gigantea were retrieved from the JGI genome portal [] using tblastn and pblast alignment algorithms []. Potential sall orthologs for the Xenoturbellid Xenoturbella, the acoels Convolutriloba and Isodiametra, the annelid Dinophilus, t […]

library_books

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

2018
mSystems
PMCID: 5893860
PMID: 29657970
DOI: 10.1128/mSystems.00039-18

[…] hort Read Archive (SRA) identifiers are provided in for all of the data sets except Iowa continuous cornfield soil. For the latter, seven lanes from one run of Illumina HiSeq were retrieved from the JGI Genome Portal (http://genome.jgi.doe.gov) on 21 July 2016 from project 402461.Nonpareil results with k-mer kernel were obtained by using a 27-in. iMac with 8 gigabytes of random-access memory and […]

library_books

Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

2018
Biotechnol Biofuels
PMCID: 5879799
PMID: 29619080
DOI: 10.1186/s13068-018-1084-1

[…] The protein encoded by Tr69957 is described as a maltose permease according to the genome database of T. reesei, available in the JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html). Considering all the parameters provided by the I-TASSER platform, the chosen model for the Tr69957 (Fig. a) was predicted based o […]

call_split

Localization and dimer stability of a newly identified microbial rhodopsin from a polar, non motile green algae

2018
BMC Res Notes
PMCID: 5781313
PMID: 29361974
DOI: 10.1186/s13104-018-3181-4
call_split See protocol

[…] Search on JGI genome portal (http://genome.jgi.doe.gov) of C. subellipsoidea for microbial rhodopsin retrieved the sequence of CsR. Alignment was performed on ClustalW [] platform using Bioedit. Transmembrane h […]

library_books

Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota

2018
Genome Biol Evol
PMCID: 5786227
PMID: 29329439
DOI: 10.1093/gbe/evy002

[…] R. irregulare using TBLASTN (). These transcriptomic and genomic data include published expressed sequence tags (ESTs) and the genome of R. irregulare isolate DAOM-197198 Version 2.0 available at the JGI Genome Portal (, ). Orthology of the R. irregulare genes was first assessed using the reciprocal best hits approach in conjunction with domain architecture analysis. Hits of e-value lower than 1E− […]

call_split

Characterization of sulfhydryl oxidase from Aspergillus tubingensis

2017
BMC Biochem
PMCID: 5721475
PMID: 29216817
DOI: 10.1186/s12858-017-0090-4
call_split See protocol

[…] I (InterPro: IPR000103) was carried out. The selected protein sequences were obtained from UniProtKB except AtSOX sequence was retrieved from the genome of A. tubingensis from Joint Genome Institute (JGI) genome portal []. The alignment of the sequences was done with MAFFT [], and alignment was trimmed with trimAl []. The aligned sequences were from Ascomycetes species except two proteins were bac […]

Citations

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JGI Genome Portal institution(s)
Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
JGI Genome Portal funding source(s)
Supported by the Director, Office of Science, Office of Biological and Environmental Research, Life Sciences Division, U.S. Department of Energy [DE-AC02-05CH11231].

JGI Genome Portal review

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Korin Albert

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Dataset
Our lab uses this resource extensively and the interface is easy to use. It has a large collection of bifidobacteria genomes, which aren't always well-represented in research databases. It's great for doing quick comparisons between several genomes without actually having to download the genome files. It's also super fast if you want to see if specific genes are found in several genomes at once.