BIOCOMPUTING LAB
Ushering in on the advances in the biological sciences and development of computer algorithms, the academics and research environment have found dedicated softwares and programs for understanding gene structure, cDNA architecture, and protein modeler complexities. Learning the basics of macromolecular assembly, positional conformation, and regulatory functions utilizing the basic and advanced informatics softwares makes for an improved understanding of the concepts in biological sciences. Furthermore, with Next-Generation Sequencing becoming easily accessible to smaller labs, the big data generated could be annotated and analyzed amicably using the Linux or Windows operating softwares. At TSBS, we provide a dedicated bio-computing lab with N-computing features for easy annotation and characterization of the gene and the protein.
The following free and licensed softwares at TSBS Bio-computing facility provides an added advantage to students pursuing studies in Biotechnology and Applied Microbiology. The students of the department are also trained in using the composite databases such as NCBI-PubMed, Protein Data Bank, EMBL-ENA and DDBJ, Japan.
LIST OF SOFTWARES
| SL.NO | SOFTWARE | APPLICATION |
| 1 | Lasergene software (Full suite) by DNASTAR Inc., Madison, Wisconsin, USA | Software for all major applications in genomics, molecular biology, and structural biology. The application of the software encompasses putative analysis of single gene or transcript to whole-genomics or transcriptomics analysis. |
| 2 | Clustal X and Clustal W software by Conway Institute, UCD, Dublin | Softwares largely used for multiple sequence alignments (MSA) to understand the conserved protein domains, motifs, and other regulatory binding sites. These softwares are even used to find the percent identity of two or more than two sequences and the distance matrix. |
| 3 | Molecular Evolution and Genetics Analysis (MEGA ver. 5.0) | A sophisticated platform for analysis of evolutionary distances in related organisms by construction of phylogenetic tree maps. The phylogenetic tree methods supported are Maximum Likelihood, Maximum Parsimony and Distance Methods. |
| 4 | GeneDoc (ver. 2.7) | The software conveniently addresses the need to select conserved domains in cDNA structure and put the same into the publication perspective. |
| 5 | FGENESH and FGENESHV | The software programs are used to detect the genes in eukaryote and prokaryote sequences. These are also used to annotate transcripts from Next-Generation Sequencing data and Single-nucleotide polymorphism discovery. |
| 6 | Matinspector, TRANSFAC, and other neural network software | For promoter sequence analysis. |
LIST OF EXPERIMENTS CONDUCTED
| Sl. No. | Topic |
| 1. | Introductory information and utilization of composite databases such as PubMed and nucleotide sequence databases such as GenBank, NCBI; EMBL, EBI; DDBJ; DNA databank of Japan |
| 2. | Overview and utilization of protein sequence databases such as NCBI nr, Swiss-Prot, PROSITE, InterPro, Pfam and others |
| 3. | Overview and utilization of protein structural databases such as PDB, Swiss-Model Repository |
| 4. | Concept of Basic Local Alignment Search Tool (BLAST) and use of BLAST tools |
| 5. | Construction of Multiple Sequence Alignment using Clustal W/Clustal X using protein sequences |
| 6. | Using MEGA 5.0 program for phylogenetic analysis using UPGMA, Maximum Likelihood (ML) and Neighbor-Joining (NJ) tree analysis |
| 7. | Use of predictive protein servers and softwares for domain analysis and bio-physical characterization |
| 8. | Understanding the components of Lasergene software for composite gene and protein analysis |
| 9. | Getting accustomed to Gene Prediction softwares such as FGENESH |
| 10. | Protein structural modeling using RASMOL/Swiss-PDB viewer |
| Beyond Syllabus Experiments | |
| 1. | Prediction of Transcription factor binding sites in the gene promoter using Transfac and MatInspector |
| 2. | Analysis of NGS data for Gene Ontology Annotations using BLAST2GO software |