Journal Article

CottonFGD: an integrated functional genomics database for cotton

Meng, Zhigang, Zhu, Tao, Liang, Chengzhen, Meng, Zhaoghong, Sun, Guoqing, Zhang, Rui, Guo, Sandui

2017

Overview

Background Cotton ( Gossypium spp.) is the most important fiber and oil crop in the world. With the emergence of huge -omics data sets, it is essential to have an integrated functional genomics database that allows worldwide users to quickly and easily fetch and visualize genomic information. Currently available cotton-related databases have some weakness in integrating multiple kinds of -omics data from multiple Gossypium species. Therefore, it is necessary to establish an integrated functional genomics database for cotton. Description We developed CottonFGD (Cotton Functional Genomic Database, https://cottonfgd.org ), an integrated database that includes genomic sequences, gene structural and functional annotations, genetic marker data, transcriptome data, and population genome resequencing data for all four of the sequenced Gossypium species. It consists of three interconnected modules: search, profile, and analysis. These modules make CottonFGD enable both single gene review and batch analysis with multiple kinds of -omics data and multiple species. CottonFGD also includes additional pages for data statistics, bulk data download, and a detailed user manual. Conclusion Equipped with specialized functional modules and modernized visualization tools, and populated with multiple kinds of -omics data, CottonFGD provides a quick and easy-to-use data analysis platform for cotton researchers worldwide.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Acids / Agriculture / Annotations / Bioinformatics / Biomedical and Life Sciences / Cotton / Data analysis / data collection / Data processing / Databases, Genetic / Downloading / Flowers & plants / Forecasting / Functional annotation / Gene expression / Gene sequencing / genes / Genetic marker / Genetic Markers / Genetic research / Genetic screening / Genetic Variation / Genome, Plant / Genomes / Genomics / Genomics and evolution / Genotype / Gossypium / Gossypium - genetics / Identification and classification / Information Storage and Retrieval / Internet / Life Sciences / Methods / Modernization / Modules / Molecular Sequence Annotation / nucleotide sequences / oil crops / Ontology / Plant Sciences / Proteins / Researchers / RNA-seq / Species / Statistical analysis / statistics / Structure-function relationships / transcriptome / Tree Biology / User interface / Variation / Visualization