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
Microsatellites are short tandemly repeated DNA sequences of 1–6 bp unit length. Ubiquitously distributed in eukaryotic and prokaryotic genomes and highly polymorphic they rapidly became the current genetic marker of choice. Their usage is wide and includes genetic mapping, population genetic analysis, DNA forensics and phylogenetics. More recently, microsatellite mutational dynamics have gained increasing interest as they have been shown to play a role in human genetic disorders and may have significant roles in the regulation of gene expression. Simple sequence repeats (SSRs) are found in most organisms, and occupy about 3% of the human genome. Although it is becoming clear that such repeats are important in genomic organization and function and may be associated with disease conditions, their systematic analysis has not been reported. This project demonstrated the utility of a computational approach for mining SSRs from ever increasing sequence information in biological sciences. There are some aspects of the project that could have been further enhanced to improve the knowledge regarding SSRs in different genomes. For example, a comparison of SSR information derived from genomic sequences with that of SSRs and the distribution of SSRs across different parts of the transcribed regions could be very valuable. However, such an analysis is currently possible only for species for which complete genomic sequence information is available and a few others for which at least some genomic coverage is achieved. Another aspect that would extend the value of the findings of this study for comparative genomics is the cross-species clustering of SSRs to understand the extent of homology and the frequency of SSRs that fall into these clusters could potentially be useful for comparative mapping studies. Microsatellites can thus firmly be expected to have an important role in genomics research in the future and mining microsatellites from sequence databases is likely to take center stage in years to come.