Bioinformatics - A Student's Companion (eBook)

K. Syed Ibrahim is Post Doctoral Fellow at the Department of Biotechnology, Mizoram University. He received his PhD in Biotechnology from Alagappa University, Karaikudi. His fields of interest include protein expression and purification, microbial ecology, high throughput sequencing and data analysis.G. Gurusubramanian is a Professor of Zoology at Mizoram University with more than 23 years of experience in teaching and research. He received his PhD in Zoology from the University of Madras, Chennai and served as Post Doctoral Humboldt Fellow at the Institut für Biologischen Pflanzenschutz, Germany. His contributions have been recognized with awards like Fellow of International Society for Ecological Communication, Poland, the Business Excellence Award from the International Business Council, and the Life Time Achievement Award from the Indian Compendium Bureau, New Delhi. He has published over 109 articles in leading peer-reviewed International journals, has contributed to two books published by leading publishers and holds four patents. He has been successful in attracting funding from various bodies like the UGC, DBT, CSIR and Central Silk Board as a Principal Investigator.Ravi Prakash Yadav is a Research Scholar at the Department of Biotechnology, Mizoram University. He received his MSc Biotechnology from the Kalinga Institute of Industrial Technology, Bhubaneswar (2010–2012). His fields of interest include Computational Biology/Bioinformatics and Cancer Genomics. Currently, he is working on the study of genomic alterations in cell cycle regulatory genes that result in tumorigenesis.Zothansanga is currently working as a postdoctoral researcher at the Department of Biotechnology, Mizoram University with 5 years of teaching experience. His fields of interest include microbial diversity and metagenomics, molecular phylogeny, bioinformatics and microbial control of pests. He is presently working on microbial community analysis using Next-Generation Sequencing methods.N. Senthil Kumar is a Professor of Biotechnology at Mizoram University with more than 12 years of experience in teaching and research. He completed his PhD in Zoology at Bharathiar University, Coimbatore and worked as a Post Doctoral Fellow at Sun Yat-sen University, Guangzhou, China. His fields of interest include bioinformatics and molecular phylogeny, cancer genomics and human genetics. With over 50 publications in reputed international peer reviewed journals and authoring two books in leading publications, his contributions have been recognized with various awards from the CSIR and DBT. As a Principal Investigator, he has successfully completed Research Projects funded by government funding bodies like the DBT, CSIR and DST.Probodh Borah is a Professor of Microbiology/Animal Biotechnology at Assam Agricultural University with more than 29 years of experience in teaching and research. He completed his PhD in Veterinary Science at Assam Agricultural University, Guwahati and served as Post Doctoral Fellow at the University of California, USA. He has over 63 publications in peer-reviewed journals and has authored six books, two laboratory manuals and contributed three book chapters. He is an active member of the DBT Committee for North Eastern States. As a Principal Investigator, he has received funding from government agencies including the UGC, DBT, CSIR, ICMR and DST. He is also the Coordinator, Bioinformatics Infrastructure Facility and State Biotech Hub (Assam). S. Karutha Pandian is a Professor of Biotechnology at Alagappa University. He received his PhD from the Forensic Sciences Department (Govt. of Tamil Nadu) affiliated with the University of Madras. After his PhD, he moved to the Centre for Cellular and Molecular Biology (CCMB), Hyderabad followed by the National Tsing Hua University, Taiwan for Post Doctoral research. An established pioneer in drug discovery from natural products, he has published 127 articles in leading peer-reviewed International (SCI) journals and has contributed to five books and two Laboratory Manuals published by leading publishers like Springer. He has been successful in completing nine Major Research Projects (MRPs) funded by government bodies like the UGC, DBT, DCI, CSIR and ICMR as a Principal Investigator. In recognition to his contributions, he has been awarded with the ‘Certificate of Achievement’ under the ‘Performance Linked Incentive Scheme’ of the Alagappa University, the ‘Shri. P.K. Das Memorial Best Faculty Award in Biotechnology’ by the Nehru Group of Institutions, and the Tamil Nadu Scientist Award (TANSA) in Biological Sciences for the year 2012.

Foreword 5
Preface 7
Contents 9
About the Authors 12
1 Nucleotide Analysis 15
1.1 Sequence Retrieval 16
1.2 Primer Designing 20
1.3 Designing Degenerate Primers 25
1.4 Reading of Sequence Trace Files Using Finch TV 28
1.5 Troubleshooting DNA Sequencing Problems 32
1.6 Editing Sequence Data 38
1.7 Sequence Assembly—CAP3 Program 42
1.8 Checking for Vector Contamination 46
1.9 Restriction Mapping Using NEBcutter 49
1.10 Gene Prediction Using ORF Finder (Open Reading Frame Finder) 54
1.11 Gene Prediction Using FGENESB 61
1.12 Dot-Plot 63
1.13 Global Sequence Alignment 70
1.14 Local Sequence Alignment 75
1.15 Basic Local Alignment Search Tool (BLAST)—Nucleotide BLAST 78
1.16 Interpreting BLAST Result 84
1.17 Multiple Sequence Alignment: T-Coffee for Small Alignments 90
1.18 Multiple Sequence Alignment—MUSCLE for Medium Alignments 98
1.19 Multiple Sequence Alignment—MAFFT for Large Alignments 101
1.20 Multiple Sequence Alignment and Phylogenetic Analysis Using MEGA 106
2 DNA Marker Analysis 131
2.1 Genetic Analysis Using NTSYSpc (Numerical Taxonomy System) 131
2.2 Principal Coordinate Analysis (PCOORDA) Using NTSYSpc 138
2.3 Population Genetic Analysis Using PowerMarker 143
2.4 Dissimilarity Analysis—DARwin5 (Dissimilarity Analysis and Representation for Windows) 148
3 RNA Analysis 154
3.1 Predicting RNA Secondary Structure 154
3.2 Finding Repeats 158
4 Protein Sequence Analysis 162
4.1 Protein Sequence Retrieval from UniProtKB 162
4.2 Visualization of Features in a Multiple Sequence Alignment 167
4.3 Predicting Signal Peptides in Proteins Using SignalP 4.1 Server 169
4.4 Predicting Transmembrane Segments and Signal Peptides in Proteins Using Phobius 175
4.5 Predicting Subcellular Location Using TargetP 179
4.6 Protein BLAST (blastp) 184
4.7 Position-Specific Iterated (PSI)-BLAST 189
4.8 Creating Pattern from Alignment 193
4.9 Pattern-Hit Initiated (PHI)-BLAST 195
4.10 Domain Enhanced Lookup Time Accelerated-BLAST (DELTA-BLAST) 198
5 Protein Structure Analysis 203
5.1 Protein Primary Structure Analysis—ProtParam 203
5.2 Protein Secondary Structure Prediction 208
5.2.1 Secondary Structure Prediction Using SOPMA 209
5.2.2 Secondary Structure Prediction Using PSIPRED 213
5.3 Protein Tertiary Structure Prediction by Homology Modelling 216
5.3.1 Homology Modelling Using SwissModel 220
5.3.2 Protein Tertiary Structure Prediction by Threading (Fold Recognition) 227
5.4 Protein Tertiary Structure Analysis 235
5.4.1 RAMPAGE 235
5.4.2 Protein Structure Analysis Using SAVeS 238
5.5 Protein Structure Visualization 242
5.5.1 RasMol 242
5.5.2 PyMol 250
5.6 Protein Structure Alignment/Superimpose Using SuperPose 258
5.7 Protein Cleft Analysis 264
6 Protein–Ligand Interactions 269
6.1 Protein–Ligand Docking Using AutoDock4.1 and MGLTools 269
6.2 Protein–Protein Docking Using ClusPro2.0 280
Appendix: Online Resources on Bioinformatics 287
References 291