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CGD specifications

Information


Unique identifier OMICS_21283
Name CGD
Alternative name Cacao Genome Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Dorrie Main
  • person_outline Ping Zheng

Additional information


http://www.cacaogenomedb.org/sites/default/files/CGD_brochure_2012.pdf

CGD citations

 (4)
library_books

Theobroma cacao L. pathogenesis related gene tandem array members show diverse expression dynamics in response to pathogen colonization

2016
BMC Genomics
PMCID: 4869279
PMID: 27189060
DOI: 10.1186/s12864-016-2693-3

[…] s []. Next, a custom Python (python.org) [] script (PRAminoacidgetterASF) was used to extract protein IDs from the BLASTp output and use them to extract the peptide sequences available in the Criollo cacao genome database.The list of amino acid sequences was uploaded to the NCBI Batch Web CD-Search Tool (v3.13) [] with an e-value cutoff of 0.01. Another script (PRdomainsorterASF) was used to sort […]

library_books

Analysis of Gene Expression and Proteomic Profiles of Clonal Genotypes from Theobroma cacao Subjected to Soil Flooding

2014
PLoS One
PMCID: 4188525
PMID: 25289700
DOI: 10.1371/journal.pone.0108705

[…] data analysis was performed using the Masslynx 4.0 software (Waters- Micromass, Manchester, UK). Protein identification was performed using a Mascot server (Version 2.1.04, Matrix Science) and the T. cacao genome database . The search criteria used were trypsin digestion, variable modifications set as cysteine (Cys) and methionine (Met), max of one missed cleavages allowed and peptide mass toleran […]

library_books

Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree

2014
Front Microbiol
PMCID: 4162356
PMID: 25309519
DOI: 10.3389/fmicb.2014.00479

[…] CDS database and 11,225 unigenes had A. thaliana identifiers and annotations with the e-value cutoff of 1*e-5 using TBLASTX. The 6022 unigenes without A. thaliana annotations were blasted against the cacao genome database using BLASTN and 4931 out of 6022 unigenes had cacao identifiers and predicted full length gene sequences. Those 4931 cacao full length gene sequences were further blasted agains […]

library_books

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

2013
Genome Biol
PMCID: 4053823
PMID: 23731509
DOI: 10.1186/gb-2013-14-6-r53

[…] gle orthologous region in the Criollo genome. The individual ORs identified using Mercator and aligned by MAVID [] can be searched and explored using the graphic synteny viewer, GBrowse_syn [] in the Cacao Genome Database []. […]

Citations

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CGD funding source(s)
Supported by Washington State University.

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