Skip to main content
eScholarship
Open Access Publications from the University of California

Gene Annotation in Rice Genome Using Homology

  • Author(s): Athakitkarnka, Pavitra
  • Advisor(s): Pellegrini, Matteo
  • et al.
Abstract

In the functional genomics era, systems-level analysis of genomic and proteomic data quickens the pace of gene-function discovery. I created a program and collected cross-referenced database for the rice genome. This program utilizes sequence similarity as a way to annotate all genes with the gene ontology (GO) terms and performs a functional analysis on genes in rice, an economically important crop with limited functional analysis tools. For demonstration purpose, application of the tool to one gene list created from cytokinin oxidase/ dehydrogenase activity reveals two GO terms that suggest the relevance for cytokinin associated terms as cytokinins was used to generate the gene list. To my knowledge, while there are tools available on the web to interpret the biological function of a gene list, none are set up for use with rice protein sequences. My program overcomes this limitation by permitting the functional analysis of rice amino acid sequences. The example gene list and code are available to reproduce the results.

Main Content
Current View