Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://chloroplast.cbio.psu.edu/
Full name: Chloroplast Genome Database
Description: The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and alignments.
Year founded: 2006
Last update: 2007-06-21
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: The Pennsylvania State University
Address: University Park, PA 16802, USA
City: Park
Province/State: PA
Country/Region: United States
Contact name (PI/Team): Claude W. dePamphilis
Contact email (PI/Helpdesk): cwd3@psu.edu

Publications

16381961
ChloroplastDB: the Chloroplast Genome Database. [PMID: 16381961]
Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, dePamphilis CW.

The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and alignments (http://chloroplast.cbio.psu.edu/). With recent technical advances, the rate of generating new organelle genomes has increased dramatically. However, the established ontology for chloroplast genes and gene features has not been uniformly applied to all chloroplast genomes available in the sequence databases. For example, annotations for some published genome sequences have not evolved with gene naming conventions. ChloroplastDB provides unified annotations, gene name search, BLAST and download functions for chloroplast encoded genes and genomic sequences. A user can retrieve all orthologous sequences with one search regardless of gene names in GenBank. This feature alone greatly facilitates comparative research on sequence evolution including changes in gene content, codon usage, gene structure and post-transcriptional modifications such as RNA editing. Orthologous protein sets are classified by TribeMCL and each set is assigned a standard gene name. Over the next few years, as the number of sequenced chloroplast genomes increases rapidly, the tools available in ChloroplastDB will allow researchers to easily identify and compile target data for comparative analysis of chloroplast genes and genomes.

Nucleic Acids Res. 2006:34(Database issue) | 54 Citations (from Europe PMC, 2021-10-23)

Ranking

All databases:
2018/5130 (60.682%)
Gene genome and annotation:
600/1366 (56.149%)
2018
Total Rank
54
Citations
3.6
z-index

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Record metadata

Created on: 2015-09-10
Curated by:
Lina Ma [2018-06-13]
Mengwei Li [2016-03-31]
Mengwei Li [2016-02-21]
Mengwei Li [2015-12-02]
Lina Ma [2015-11-25]