Course Name: Skill Course - Introduction to Computational Biology
Skill Course – Introduction to Computational Biology
Teacher
Dr. Pushpalatha Ganesh
Category
Skill Courses
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Code(Credit) : CUTM3108(0-2-2)
Course Objectives:
To foster the students with in silico bioinformatics education for their future career.
Learning Outcome:
• To learn the basic concepts of Bioinformatics and its significance in Biological data analysis.
• To inculcate the advanced tools and databases of genomics and its applications.
• To obtain the hands-on-training in in silico basics related to functional genomics.
Module I:
Unit 1: History, Scope and Importance, Databases- Tools and their Uses,
Unit 2: Introduction to various tools and databases - DNA Databases - NCBI and its GenBank resources, KEGG and its resources, DNA Data Bank of Japan (DDBJ).
Unit 3: National Centre for Biotechnology Information (NCBI): cDNA libraries and Expressed Sequence Tags (ESTs), EST analysis, Pairwise alignment techniques, Multiple sequence alignment.
Unit 4: Kyoto Encyclopedia of Genes and Genomes (KEGG): Modules, Network, Genomes, Genes and KEGG analysis tools.
Unit 5: DNA Data Bank of Japan (DDBJ): Sequence Alignment Methods, Predictive Methods Using DNA Sequences.
Module II:
Unit 1: Protein Information Resources (PIR)
Unit 2: SWISS PROT and Protein Data Bank (PDB): Protein features and motifs, annotation and curation, protein structure analysis.
Module III:
Unit 1: Phylogenetic analysis: Evolution, elements of phylogeny, methods of phylogenetic analysis, Phylogenetic tree of life, comparison of genetic sequence of organisms, phylogenetic analysis tools-Phylip, ClustalW.
Unit 2: BLAST: Basic Local Alignment Search Tool: Nucleotide BLAST, Protein BLAST, Blastn, Blastp, Blastx, tBlastn, tBlastx
Unit 3: Sequence Alignment: MSA using conserved domain and local sequence similarity information, COBALT, Protein sequence alignment, Nucleotide sequence alignment.
Module IV:
Applications of bioinformatics tools in Agriculture, Medicine, Diary, Health Industry, Environment, Biotechnology, Genomics, Transcriptomics and Proteomics; Bioinformatics and Career.
Suggested Readings:
- Attwood TK & Parry-Smith DJ. 2003. Introduction to Bioinformatics. Pearson Education.
- Rastogi SC, Mendiratta N & Rastogi P. 2004. Bioinformatics: Concepts, Skills and Applications. CBS.
- Arthur M.Lesk, Introduction to Bioinformatics, Oxford University Press, New Delhi, 2003.
Session Plan
Practice 1:
Computational Biology: History, Scope and Importance, Databases - Tools and its applications.
Practice 2:
DNA Databases - NCBI and its GenBank resources
Practice 3:
DNA Databases - KEGG and its resources
Practice 4:
DNA Databases - DNA Data Bank of Japan
Practice 5:
cDNA libraries and Expressed Sequence Tags (ESTs)
Practice 6:
Expressed Sequence Tags (ESTs)
Practice 7:
Pairwise alignment techniques
Practice 8:
Multiple sequence alignment
Practice 9:
Kyoto Encyclopedia of Genes and Genomes (KEGG): Modules, Network, Genomes, Genes and KEGG analysis tools
https://www.youtube.com/watch?v=CvnmcH7jt1Y
Practice 10:
DNA Data Bank of Japan (DDBJ): Sequence Alignment Methods, Predictive Methods Using DNA Sequences.
Practice 11:
Protein Information Resources (PIR)
Practice 12:
SWISS PROT and Protein Data Bank (PDB): Protein features and motifs, annotation and curation, protein structure analysis.
https://www.youtube.com/watch?v=GwHnoqwwi0I
Practice 13:
Phylogenetic analysis.
Practice 14:
Evolution, elements of phylogeny, methods of phylogenetic analysis
Practice 15:
Phylogenetic tree of life, comparison of genetic sequence of organisms
Practice 16:
Phylogenetic analysis tools-Phylip
Practice 18:
BLAST: Basic Local Alignment Search Tool
Practice 19:
Nucleotide BLAST
Practice 20:
Protein BLAST
Practice 21:
Blastn, Blastp, Blastx, tBlastn, tBlastx
https://www.youtube.com/watch?v=7eVPd4SAiSw
Practice 22:
Sequence Alignment
Practice 23:
MSA using conserved domain and local sequence similarity information
Practice 24:
Sequence Alignment: COBALT
Practice 25:
Protein Sequence Alignment
Practice 26:
Nucleotide Sequence Alignment
Practice 27:
Applications of bioinformatics tools in Agriculture
Practice 28:
Applications of bioinformatics tools in Medicine
Practice 29:
Applications of bioinformatics tools in Health Industry
Practice 30:
Applications of bioinformatics tools in Diary
Practice 31:
Applications of bioinformatics tools in Environment
Bioinformatics-applications-in-life-and-environmental-sciences
Practice 32:
Applications of bioinformatics tools in Biotechnology
Practice 33:
Applications of bioinformatics tools in Genomics
Practice 34:
Applications of bioinformatics tools in Transcriptomics
Practice 35:
Applications of bioinformatics tools in Proteomics
Practice 36:
Bioinformatics and Career
Projects:
- Genome-wide identification of specific genes in medicinal plants.
- In silico identification of anti-bacterial specific genes in medicinal plants.
Our Main Teachers
Dr. Pushpalatha Ganesh, Professor & Head in the Department of Plant Biotechnology, M. S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, Odisha, India. She possesses more than 11 years of research and teaching experience in Agricultural Biotechnology and Crop Physiology at several national level organizations including DRR, Hyderabad and NRCPB, IARI, […]