Project titles for:
Project titles for: 2009-11
- Simple Sequence Repeat Finder Tool/ Software
- Diversity in various visualization tools for biological molecules
- Comparison of Online Tools for Transposon Element Detection
- Online Resources for Annotation of Rice Genome
- Computational Gene Finding in Rice
- Predicting Protein Structure using only Sequence Information
- Pathological Database of Crops
- Benchmarking of Alignment Algorithms
- Promotor Discovery in Rice Genome
Adenylate Uridylate- rich elements are distinct sequence elements in 3`Untranslated Regions of mRNA., often consisting of one or several AUUUA pentamer located in Adenine and Uridine rich regions. Rice is an excellent model plant for genomics, as it has the smallest genome with an estimated size of 430 megabase pairs (Mbp) as compared to the significantly large genome sizes of other crop plants. The biggest region behind choosing this plant as basic material was that the whole genome of rice has been sequenced. Thus in silico finding of well annotated sequence would be found to be more informative. Objective behind finding ARE sites in rice genome was that AREsites were found to be involved in modulation of mRNA’s stability and translational efficiency. So they may be involved in special protein production during stress conditions in rice e.g. Scarcity of water, macro and micro nutrient’s Scarcity etc. AREsites may be also found to be involved in diseased conditions like tumors and other uncontrolled cell productions. So finding AREsites in important staple plant like rice may be beneficial in improving rice varieties by removal of these particular sequences from rice genome and also finding such important motifs may lead to significant research activities which may help in generating disease resistant or water and environment stress resistant varieties of rice. Methodology followed was very simple, and effective. Source data was taken from NCBI, 3`UTR was found by using UTRdb database, characteristic motif was found by using prosite database. Results obtained were embedded in HTML codes and Information display was generated. ARE-R was first approach which gave an easy access to the AREsites present in the genome of Oryza sativa ssp. japonica. The results were made easy to use for further experiments as these were given chromosome wise and each result was hyperlinked with the Genbank entry so that the details of that particular gene could be retrieved by one click only. As importance of AREsite was highlighted in previous years by in silico and in vivo experiments in human and mouse genome to a great extent, it was also expected that ARE must have some significant role in rice too.