Abstract
The Plant Gene Index (PlantGI) database is developed as a web-based search system with search capabilities for keywords to provide information on gene indices specifically for agricultural plants. The database contains specific Gene Index information for ten agricultural species, namely, rice, Chinese cabbage, wheat, maize, soybean, barley, mushroom, Arabidopsis, hot pepper and tomato. PlantGI differs from other Gene Index databases in being specific to agricultural plant species and thus complements services from similar other developments. The database includes options for interactive mining of EST CONTIGS and assembled EST data for user specific keyword queries. The current version of PlantGI contains a total of 34,000 EST CONTIGS data for rice (8488 records), wheat (8560 records), maize (4570 records), soybean (3726 records), barley (3417 records), Chinese cabbage (3602 records), tomato (1236 records), hot pepper (998 records), mushroom (130 records) and Arabidopsis (8 records). The database is available for free at http://www.niab.go.kr/nabic/.
Highlights
The gene indices use available expressed sequence tag (EST), tentative consensus (TC), expressed transcript (ET) and gene sequences along with a reference genome
Gene index is constructed for species organisms by first clustering, assembling EST and annotated gene sequences
Dataset: The EST data was collected for Chinese cabbage and rice genome project at National Institute of Agricultural Biotechnology (NIAB) (127,144 EST)
Summary
The gene indices use available expressed sequence tag (EST), tentative consensus (TC), expressed transcript (ET) and gene sequences along with a reference genome. Gene index is constructed for species organisms by first clustering, assembling EST and annotated gene sequences. The importance of EST assembly and clustering has been well established as evidenced by databases such as XGI [4] and TGI database [3]. Methodology: Dataset: The EST data was collected for Chinese cabbage and rice genome project at NIAB (127,144 EST). Database content: PlantGI database provides 34,000 EST CONTIGS information for 10 species namely, rice (8488 records), wheat (8560 records), maize (4570 records), soybean (3726 records), barley (3417 records), Chinese cabbage (3602 records), tomato (1236 records), hot pepper (998 records), mushroom (130 records) and Arabidopsis (8 records)
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