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
Comparison and alignment of a series of proteins and DNA sequences among the first and are now established as the most powerful and frequently used bioinformatics methods. A variety of as a computational algorithms and programs have been created for this purpose. Over past 10 years, more than 50 alignment methods and/or packages have been developed .This raises the question of which method to use and what criteria should be used in comparing methods. The major way in which new packages have been compared is from performance on sets of benchmark test cases BAliBASE. Probcons achieves the highest scores in all but one BAliBASE test (BBS12), however, when full length sequences were used in the test cases, inmost cases the optimal aligner incorporated local alignment strategies (FINSi and PCMA). Also from BBS and BB subsets that all methods experience difficulties in aligning sequences of low identity the average improvement in Column score experienced go from BBS (0-20%) to BBS (20-40%) is 43.54%; going from BB11 to BB12; relative improvement increases to 55.16%. For Oxbench, Homstrad datasets, test cases were categorized with respect to sequence percent identity. As in the case of BAliBASE, local methods like FINSi achieved the highest score when test cases containing full-length sequences of lower identity were used, while Probcons became the optimal aligner for the later categories in OxBench. For Homstrad, Probcons again was the most accurate alignment method in all but the last categoery, where T-Coffee and ClustalW both outperformed Probcons.