ChloroplastDB: the Chloroplast Genome Database.

Liying Cui, Narayanan Veeraraghavan, Alexander Richter, Kerr Wall, Robert K. Jansen, Jim Leebens-Mack, Izabela Makalowska, Claude Walker Depamphilis

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalNucleic acids research.
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006

Fingerprint

Chloroplast Genome
Databases
Chloroplast Genes
Genes
RNA Editing
Names
Plastid Genomes
Genome
Molecular Sequence Annotation
Proteins
Nucleic Acid Databases
Chloroplasts
Codon
Organelles
Research Personnel

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Cui, L., Veeraraghavan, N., Richter, A., Wall, K., Jansen, R. K., Leebens-Mack, J., ... Depamphilis, C. W. (2006). ChloroplastDB: the Chloroplast Genome Database. Nucleic acids research., 34(Database issue).
Cui, Liying ; Veeraraghavan, Narayanan ; Richter, Alexander ; Wall, Kerr ; Jansen, Robert K. ; Leebens-Mack, Jim ; Makalowska, Izabela ; Depamphilis, Claude Walker. / ChloroplastDB : the Chloroplast Genome Database. In: Nucleic acids research. 2006 ; Vol. 34, No. Database issue.
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Cui, L, Veeraraghavan, N, Richter, A, Wall, K, Jansen, RK, Leebens-Mack, J, Makalowska, I & Depamphilis, CW 2006, 'ChloroplastDB: the Chloroplast Genome Database.', Nucleic acids research., vol. 34, no. Database issue.

ChloroplastDB : the Chloroplast Genome Database. / Cui, Liying; Veeraraghavan, Narayanan; Richter, Alexander; Wall, Kerr; Jansen, Robert K.; Leebens-Mack, Jim; Makalowska, Izabela; Depamphilis, Claude Walker.

In: Nucleic acids research., Vol. 34, No. Database issue, 01.01.2006.

Research output: Contribution to journalArticle

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AU - Veeraraghavan, Narayanan

AU - Richter, Alexander

AU - Wall, Kerr

AU - Jansen, Robert K.

AU - Leebens-Mack, Jim

AU - Makalowska, Izabela

AU - Depamphilis, Claude Walker

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Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J et al. ChloroplastDB: the Chloroplast Genome Database. Nucleic acids research. 2006 Jan 1;34(Database issue).