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Protocols

ChromDB specifications

Information


Unique identifier OMICS_21009
Name ChromDB
Alternative name The chromatin database
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Aspergillus fumigatus
    • Candida albicans
    • Carica papaya
    • Oryza sativa
    • Populus trichocarpa
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
    • Vitis vinifera
    • Zea mays

Maintainer


  • person_outline Carolyn Napoli

Additional information


http://www.chromdb.org/help/help.html

Publication for The chromatin database

ChromDB citations

 (10)
call_split

MoJMJ1, Encoding a Histone Demethylase Containing JmjC Domain, Is Required for Pathogenic Development of the Rice Blast Fungus, Magnaporthe oryzae

2017
PMCID: 5378440
PMID: 28381966
DOI: 10.5423/PPJ.OA.11.2016.0244
call_split See protocol

[…] analyzed at Comparative Fungal Genetic Platform (CFGP; http://cfgp.snu.ac.kr) and National Center for Biotechnology Information (NCBI). Sequences of JmjC domain-containing protein were obtained from ChromDB database (www.chromdb.org). Analyses using Hidden Markov Model (HMM) profiling (http://hmmer.janelia.org) were performed to search for additional JmjC proteins in M. oryzae and to compare the […]

library_books

The Core Subunit of A Chromatin Remodeling Complex, ZmCHB101, Plays Essential Roles in Maize Growth and Development

2016
Sci Rep
PMCID: 5137073
PMID: 27917953
DOI: 10.1038/srep38504

[…] amino acid sequences of SWI3 in A. thaliana were subjected to Blastp searches against the genomic database in Zea mays (http://www.maizegdb.org/), Sorghum bicolor (http://www.plantgdb.org/SbGDB/) and the Chromatin Database (http://chromdb.org/). Conserved domain analysis was performed using CDD program (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). The phylogenetic trees were constructed u […]

library_books

Genome wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit blue mold infection process

2015
Front Plant Sci
PMCID: 4525380
PMID: 26300904
DOI: 10.3389/fpls.2015.00607

[…] The HM protein sequences from Arabidopsis, rice and maize were collected from ChromDB database. Each HM family including citrus HMs was aligned with ClustalW program. The generated files were subjected to phylogenic analysis by using MEGA 5.05 program with Neighbor-Joining meth […]

library_books

Genome wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles

2013
BMC Genomics
PMCID: 3567966
PMID: 23356725
DOI: 10.1186/1471-2164-14-57

[…] The protein sequences of histone modifiers (HMs) from Arabidopsis thaliana, Oryza sativa and Zea mays were retrieved from ChromDB (http://www.chromdb.org) and are listed in Additional file . In order to complete the catalogue of Arabidopsis HAGs and of maize JMJs, the TAIR10 (http://www.arabidopsis.org) and Zmays166 (htt […]

library_books

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

2012
PLoS One
PMCID: 3420876
PMID: 22916204
DOI: 10.1371/journal.pone.0043047

[…] dentify the most inclusive set of noncoding RNAs.To validate the Python pipeline and compare it with CPC, a set of 199 lncRNAs from www.lncrnadb.com and the set of 248 protein coding transcripts from ChromDB were run through each method of noncoding RNA detection. The Python pipeline identified 121 of 199 lncRNAs as noncoding, equivalent to an accuracy of 61 percent. The Coding Potential Calculato […]

call_split

Phylogenetic analysis and classification of the Brassica rapa SET domain protein family

2011
BMC Plant Biol
PMCID: 3264562
PMID: 22168908
DOI: 10.1186/1471-2229-11-175
call_split See protocol

[…] Sequences of SET-domain proteins from A. thaliana, O. sativa, O. tauri and S. cerevisiae were retrieved from the Chromatin Database with the key word SDG in species database respectively (ChromDB, http://www.chromdb.org). These sequences, primarily those from A. thaliana and O. sativa, were used as queries t […]

Citations

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ChromDB institution(s)
BIO5 Institute, University of Arizona, Tucson, AZ, USA
ChromDB funding source(s)
Supported by a grant from the National Science Foundation Plant Genome Research Project (#DBI- 0421679) and The ChromDB server is hosted by the Biotechnology Computing Facility at the University of Arizona.

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