Basics of Bioinformatics is a concise yet inclusive book of bioinformatics for understanding of the essentials of genomics and bioinformatics, and to integrate this with use of computational platforms. Written for students and researchers wishing to develop their knowledge of bioinformatics to facilitate their own research, the basics of genomics and bioinformatics are explained in simple context, followed by practical use of computational tools available to solve biological research problems. Important areas of bioinformatics including mining of biological databases, sequence alignment, gene prediction, molecular phytogenetics, structural bioinformatics, genomics and proteomics are described in the book. The book does not emphasizes the details of computer science or sophisticated programming skills but supports the need of students and researchers wishes to analyse bioinformatics problems. Technical details of work algorithms are explained with a minimum use of mathematical formulas and with graphical illustrations to aid understanding. The authors believe that the book will be useful for easy grasping of computational ideas and subsequent use of existing bioinformatics tools more effectively, and advancement of research goals by envisioning new computational goals in biological researches
Dr. Sachinandan De Principal Scientist and Incharge Animal Biotechnology Center National Dairy Research Institute, Karnal-132001 Haryana, India
Dr. Biswajit Brahma Associate Professor Division of Livestock Production & Management Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu & Kashmir-181102, India
1. Genome Organization and Analysis ................................................. 1 B.R. Yadav (Retd.)
2. Polym orphism in Protein and DNA ............................................... 11 Sachinandan De and B. Brahma
3. Polymerase Chain Reaction .............................................................. 21 Shamik Polley, Jaspreet Singh Arora, Ramakant Kaushik, Vinesh P.V., Sunil More and Sachinandan De
4. Real Time PCR Quantitation ............................................................ 29 Parveen Kumar, Arpana Verma and T.K. Datta
5. Using RT-PCR and Quantitative Competitive PCR for Studying Differential Gene Expression in Oocytes and Embryos ................................................................ 39 T.K. Datta and Sachinandan De
6. Single Nucleotide Polymorphism in Human Heat Shock Protein Genes ........................................................................... 51 Taruna Anand and Dharmendra Kumar
7. Proteomic Approaches for Identification, Analysis and Characterization of Biological Macromolecules for Application in Animal Science .................................................. 61 Ashok K. Mohanty
8. Protein Folding and Stability ............................................................ 73 Jai K. Kaushik
9. Multiple Sequence Alignment Using Clustal W and Clustal X ....................................................................................... 87 Shamik Polley, Jaspreet Singh Arora, Vinesh P.V., Sunil More and Sachinandan De
10. Primer Designing ................................................................................ 95 Arpana Verma, Sandeep Rajput, Parveen Kumar and Bhaskar Roy
11. BLAST: Basic Local Alignment Search Tool ................................103 Annu Yadav and Paras Yadav
12. In Silico Genome Analysis ...............................................................111 S.K. Sood, Puja Lather and Mehak Dangi
13. Sequence Manipulation Suite .........................................................117 Jaspreet Singh Arora, Vinesh P.V., Shamik Polley, Sunil More and Sachinandan De
14. Sequence Analysis Using Bioedit ...................................................127 Vinesh P.V., Shamik Polley, Jaspreet Singh Arora, Sunil More and Sachinandan De
15. NEBcutter...........................................................................................135 Sunil More, Shamik Polley, Jaspreet Singh Arora, Vinesh P.V. and Sachinandan De
16. DNA Methylation .............................................................................141 Sandeep Rajput and T.K. Datta
17. Eukaryotic Gene Prediction Methodology ...................................149 Bhaskar Roy, Sandeep Rajput, Arpana Verma, Parveen Kumar and T.K. Datta
18. Eukaryotic Promoter Prediction.....................................................157 Bhaskar Roy, Sandeep Rajput, Arpana Verma, Parveen Kumar and T.K. Datta
19. Phylogenetic Analysis Using the Phylip Package .......................169 Bhaskar Roy, Sandeep Rajput and T.K. Datta
20. Emboss: An Open Source Comprehensive Bioinformatics Suite of Programs for Everyone and Everything ........................185 Aruna Pandey
21. Insilico Reconstruction of Phenylalanine Metabolic Pathways ............................................................................................189 Aruna Pandey
22. Single Strand Conformation Polymorphism (SSCP) A Technique for SNP and Mutation Detection ...........................193 Ramakant Kaushik, Shamik Polley, Jaspreet Singh Arora, Vinesh P.V., Sunil More and Sachinandan De
23. Microsatellite Markers-tools for Livestock Genetic Analysis ....201 R. Arora and S. Bhatia
24. Soft Computing Tools for Bioinformatics Applications .............211 A.K. Sharma
