RICD: a rice indica cDNA database resource for rice functional genomics

Area of Science:

• Genomics
• Bioinformatics

Background:

• The indica subspecies of Oryza sativa L. is the most cultivated rice globally.
• Extensive cDNA libraries from Guangluai 4 and Minghui 63 varieties yielded over 20,000 full-length cDNAs and 40,000 ESTs.
• A need existed for a centralized data source for these indica rice cDNA clones.

Purpose of the Study:

• To develop a comprehensive online database for rice indica cDNA clones.
• To provide researchers with a user-friendly platform for accessing and analyzing indica rice genetic information.
• To support functional genomics and comparative studies of the indica rice subspecies.

Main Methods:

• Construction of an online MySQL-PHP driven database.
• Implementation of a user-friendly web interface for data retrieval.
• Integration of diverse data types including sequences, annotations, and similarity search results.

Main Results:

• The Rice Indica cDNA Database (RICD) offers query capabilities via keywords, genome position, and sequence data.
• RICD provides detailed information including sequences, protein domain annotations, SNPs, and InDels.
• Hyperlinks to external resources like RAP-DB, TIGR, RiceGE, and Gramene enhance data utility.

Conclusions:

• The RICD serves as a valuable cDNA resource for researchers studying indica rice.
• The database facilitates functional analysis and comparative genomics of the indica subspecies.
• RICD is publicly accessible online at http://www.ncgr.ac.cn/ricd.