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Protocols

Phytozome specifications

Information


Unique identifier OMICS_03242
Name Phytozome
Restrictions to use None
Version 10.3
Maintained Yes

Documentation


Maintainer


  • person_outline David M. Goodstein

Publication for Phytozome

Phytozome citations

 (1308)
library_books

Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing end tracking protein

2018
PLoS Genet
PMCID: 5944918
PMID: 29746462
DOI: 10.1371/journal.pgen.1007221

[…] Protein sequences for CLoG1 protein homologues were identified by BLAST (default settings) in the Phytozome web portal (phytozome.jgi.doe.gov) or the ENTREZ web portal (blast.ncbi.nlm.nih.gov). In most cases only a single gene locus was identified. This is consistent with results from the Panther […]

library_books

Systematic analysis of DEMETER like DNA glycosylase genes shows lineage specific Smi miR7972 involved in SmDML1 regulation in Salvia miltiorrhiza

2018
Sci Rep
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] Unrooted neighbor-joining (NJ) trees were constructed using MEGA (version 7.0) with 1000 bootstrap replicates. Protein sequences of DMLs from 16 plant species were downloaded from Phytozome (http://phytozome.jgi.doe.gov/pz/portal.html) (Table ). Ka and Ks values were calculated for two gene pairs, SmDML2/SmDML3 and SmDML5/SmDML6, using DNASP5 software. […]

call_split

Genome wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

2018
Sci Rep
PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0
call_split See protocol

[…] database. The pHMMER search function was used, with the A. thaliana SBP domain (Pfam: PF03110) sequence as the query. The IPK Barley BLAST server (http://webblast.ipk-gatersleben.de/barley_ibsc/) and Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Hvulgare_er) databases were also searched by performing TBLASTN using SBP domain sequence as a query. The HvSPL gene accession n […]

library_books

Long non coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

2018
BMC Plant Biol
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] Genes and lncRNAs were predicted based on the switchgrass genomic database (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvirgatum) []. Differentially expressed genes and lncRNAs were identified using the following threshold values: q value ≤0.05 and | log (base2) fol […]

library_books

Prediction of plant lncRNA by ensemble machine learning classifiers

2018
BMC Genomics
PMCID: 5930664
PMID: 29720103
DOI: 10.1186/s12864-018-4665-2

[…] transcripts were subjected to less rules for lncRNA identification, the stacking method is expected to have higher accuracy. Further, this work was tested only on sequence information available from Phytozome v10.3 in order to compare predictions directly to GreeNC. Additional transcript sequences available in public repositories, or from researchers’ own sequencing libraries, would add to the nu […]

call_split

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] ax Wm82.a2.v1 (Fabaceae, Fabales) (), F. vesca v1.1 (Rosaceae, Rosales) (), and P. andersonii and T. orientalis (Cannabaceae, Rosales) from the Fabid clade (Dataset S2). Sequences were retrieved from phytozome (www.phytozome.net). […]


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Phytozome institution(s)
U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA; The Center for Integrative Genomics, University of California, Berkeley, CA, USA
Phytozome funding source(s)
This work was performed at the U.S. Department of Energy Joint Genome Institute, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional funding was provided by the Gordon and Betty Moore Foundation.

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