ABSTRACT
We have constructed the Rice Genome Information Service System (RGISS), which is an information service system of the Oryza sativa L. ssp. japonica (rice) genome, using the released version of rice Build 3.0 pseudomolecules based on the Ensembl architecture. The nonredundant library, composed of 3,360 clones of BACs, PACs, and fosmids, was used to construct supercontigs. RGISS contains 50,717 annotated genes from GenBank, 56,161 predicted genes from FgeneSH, and information on 9,587 markers, which includes STS, SSR, and EST-based RFLP. The 20,180 ESTs sequenced by the Korea National Institute of Agricultural Biotechnology (NIAB) were aligned and mapped into 168,792 exons. By gene ontology analysis, the classified protein numbers in the rice genome were 6158, 4531, and 12,364 proteins, which were mapped to molecular function, cellular component, and biological process, respectively.
Subject(s)
Biological Phenomena , Biotechnology , Clone Cells , Databases, Nucleic Acid , Exons , Expressed Sequence Tags , Gene Ontology , Genome , Information Services , Korea , Polymorphism, Restriction Fragment Length , OryzaABSTRACT
Many visualization tools have been designed to aid information processing during whole genome projects. We have developed a trace viewer program, ChroView, which can read a chromatogram file and display the chromatogram traces of the four bases. The program can be used to examine sequencing quality and base-calling errors. It can also help researchers to edit and save base-calling results while browsing the traces. Additionally, this program has a basecalling feature which can produce supplementary data for validation of the results from other base-calling programs.