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
Visualization of bio-molecules like DNA, RNA, proteins and their interaction among themselves is now becoming most frequently used approach in exploring the molecule in the field of bioinformatics. A large number of visualization tools have been developed and are available online. Taking a decision about which tool to be used for visualization now has become a conflicting job in itself. Therefore, a comparison study for the different visualization tools is necessary to make sure the tool provide best results in an accurate way for a particular job. The present study addressed different features of visualization tools (Cn3D, RASMOL, PYMOL, CHIMERA, and SWISS-PDB VIEWER) in relation to bio-molecules visualization. All tools have some common features and perform similar task by different approaches as in structure alignment all tools except RASMOL gave structure alignment but PYMOL gave best alignment with best RMSD value and Cn3D gave function of alignment editing. Similarly SWISS PDB VIEWER gave best Ramachandran plot for its ease of interpretation. While some of the features are restricted only to particular visualization tool like to find distorted residue one can use only SWISS PDB VIEWER, to perform homology Modelling SWISS PDB VIEWER and CHIMERA can be used, to find rotamers for a residue PYMOL and CHIMERA are used and to find contact and clashes in bio-molecule complexes CHIMERA and SWISS PDB VIEWER are helpful. To have in depth knowledge of bio-molecules, to know about features like ligand-protein interaction and displaying parts of bio-molecules according to their hydrophobicity RASMOL was found to be best. For publication of images and creating animation PYMOL is best suited. As no single tool was good for all the parameters of visualization, so different tools and their combinations should be used depending on the query and to get best result.