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
Transposable elements are genomic sequences which move from one site to the other site in the genome of organism and lead to mutations causing harmful effects. In the underlying project, the comparison of eight online tools is done for detection of transposable elements. These are TECLASS, REPEAT MASKER, LTR_FINDER, PLOTREP, CENSOR, MUST, HELITRON FINDER, and GYPSY. All tools are based on four different approaches for the detection of TEs: de-novo based, structure based, homology based and comparative genomics. Algorithms used to design the tools are SWAT, LIBSVM and suffix arrays. The sequence of chromosome no.12 of O.sativa japonica of 27.5 Mb was downloaded from NCBI database in Fasta format. It was used as input sequence taking the default parameters in all the tools to compare the results for transposable element detection. Output of the tools was in either text or html format. Censor and Repeat Masker gave better results as compared to the other programs. Out of Censor and Repeat Masker, better results were of Censor as it detected more number of TEs providing sequence of detected TE, its location in query sequence, alignment file, masked file and annotation file. But MITEs were not detected by Censor program. For detection of MITEs, MUST program was used.