Arabidopsis Thaliana

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Project Proposal: AIMS - Bioinformatic approach to aid gene identification and characterisation in Arabidopsis thaliana - Evaluate and integrate the accuracy of Arabidopsis database INTRODUCTION: Arabidopsis thaliana is a model plant for research and has been used wisely to study many aspects of plant biology. There is significant amount of information about this plant in the database, such as fully sequenced and annotated genomic sequence, extensive expressional data and functional characterisation data. This project aims at using such information to aid gene identification. The project will focus on a specific region (between AGIs 18,500,000 & 19,800,000) on Chromosome V, where a gene involved in root development has been mapped. OBJECTIVES: The project has three types of objectives they are: 1) To identify all possible genes in the region and most importantly to check whether there are genes mis- or incorrectly-annotated using sequence analyses 2) To establish the expression patterns and regulations of the genes using available microarray data. 3) And literature search of evidence for the functional properties of the genes of their homologues. The analyses will help to build an integrated picture which shows the genes in the region together with their expression profiles and functional properties. Such information can be used to guide our experimental strategy towards the identification of the interested gene and will provide a case-study for using bioinformatics approach to aid traditional genetic approach in gene identification. Biological Background of Arabidopsis thaliana Arabidopsis thaliana is a unique among plant model organisms due to its short life Cycle (Heh and Bülow 2008 ) and... ... middle of paper ... ...S. Kaul, et al. (1999). "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Nature 402(6763): 761-768. Meinke, D. W., J. M. Cherry, et al. (1998). "Arabidopsis thaliana: A Model Plant for Genome Analysis." Science 282(5389): 662-682. Rhee, S. Y., W. Beavis, et al. (2003). "The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community." Nucl. Acids Res. 31(1): 224-228. Sato, S., H. Kotani, et al. (1997). "Structural Analysis of Arabidopsis thaliana Chromosome 5. I. Sequence Features of the 1.6 Mb Regions Covered by Twenty Physically Assigned P1 Clones." DNA Res 4(3): 215-219. Tabata, S., T. Kaneko, et al. (2000). "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana." Nature 408(6814): 823-826.
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