ISPUB.COM The Internet Journal of Genomics and Proteomics Volume 4 Number 1 1 of 5 Protocol of Rice Genome Annotation through Comparative Functional Genomics Approach S Kushwaha, M Shakya Citation S Kushwaha, M Shakya. Protocol of Rice Genome Annotation through Comparative Functional Genomics Approach. The Internet Journal of Genomics and Proteomics. 2008 Volume 4 Number 1. Abstract Identification & characterization of genes and proteins are very important task, but these are slow processes as compared to the genome sequencing due to lack of annotation protocol. In this paper, efforts have been made to characterize Oryza sativa var. Japonica genome on the basis of comparative functional genomics. Various online tools are used in order to annotate the hypothetical sequences of rice for characterization and depiction of sub-cellular location. The results obtained from the bioinformatics tools are compared statistically through confidence score for high specificity and sensitivity. In the present study chromosome-1 is studied for rice genome interpretation, which consists of 500 hypothetical proteins. Results showed that chromosome-1 is characterized by Nuclear (50%) Mitochondrial (21%), Plastid (12%), Secretary Protein (2%) Plasma Membrane (6%), Cytoplasmic (5%), Ext. Cellular Proteins (4%) with eleven ESTs, which are concerned to root and their homologs are present in the chromosome 2, 4 and 9. INTRODUCTION Genome sequencing of animals, plants and microbes is going very fast and genomic data increasing at very rapid rate., So storage of data and transformation of these data into information are critically needed. Genomic analysis of cereal crops like rice, wheat and maize, will contribute greatly to improvement to their productivity. Rice genome is very important among the cereal crops because of its small genome size (430 Mb) and high degree of chromosomal co- linearity with other cereal crops [ 22 ] like maize, wheat, barley and sorghum. It is a major food supply source for more than half of the world's population. In the countries like Asia, Africa, and Latin America where the demand for rice is at the top priority, the population is continuously increasing [ 9 ]. There is need to develop novel techniques to breed new varieties of rice. Following the successful completion of human genome project, a new era of whole genome science has emerged ranging from humans to plants and yeast [ 4 ]. Comparisons between distantly related genomes provide insight into the universality of biological mechanisms and identify experimental models for studying complex processes. The IRGSP, a public consortium of publicly funded laboratories has generated finished quality sequence of the entire genome using the clone-by clone sequencing strategy [ 13 , 21 ] and made it available to public domain. With the completion of the sequencing process, annotation is a dynamic process essential to add the value to the genome [ 2 , 4 , 5 ]. The major task in genome annotation is to identify the genes termed as structural annotation, which relies on the computational methods. Considering the importance of comparative genetics in the forefront of new knowledge on plant genomes and genes, comparative bioinformatics remains an essential strategy to gain new insights on the needs and expectations on rice genomics. The information regarding genes, their proteins and their specificity is obtained from cellular and subcellular locations of proteins [ 1 , 8 , 3 ]. Bioinformatics approaches are helping in expedite the determination of protein cellular and subcellular locations [ 10 , 11 , 12 , 14 ]. To explore this problem, proteins were classified [ 6 ], according to their specific characterization and subcellular locations [ 16 , 17 , 19 ], into the following 12 groups: (1) Chloroplast, (2) Cytoplasm, (3) Cytoskeleton, (4) Endoplasmic Reticulum, (5) Extracellular, (6) Golgi Apparatus, (7) Lysosome, (8) Mitochondria, (9) Nucleus, (10) Peroxisome, (11) Plasma Membrane (12) Vacuole. ESTs are c-DNA clone that has been arbitrarily chosen and subjected to single-pass sequencing in both directions, which gives us a rough canvassing of a tissue or organisms transcriptional content [ 7 ]. They provide a highly cost & time effective method of accessing the desired feature. The cellular location (tissue) identification by the ESTs (japonica