Skill Course – Introduction to Computational Biology

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Dr. Pushpalatha Ganesh

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Skill Courses

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Course Name: Skill Course - Introduction to Computational Biology

 

 

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.

https://www.youtube.com/watch?v=v1cTNhiZ2_c

Practice 2:
DNA Databases - NCBI and its GenBank resources

https://www.youtube.com/watch?v=-dOQMiEtL8I

Practice 3:
DNA Databases - KEGG and its resources

https://www.youtube.com/watch?v=JOzWbpauw1o

Practice 4:
DNA Databases - DNA Data Bank of Japan

https://www.youtube.com/watch?v=UF640aBB_c0

Practice 5:
cDNA libraries and Expressed Sequence Tags (ESTs)

https://www.youtube.com/watch?v=RHz2nZbzjpA

Practice 6:
Expressed Sequence Tags (ESTs)

https://www.youtube.com/watch?v=QIZ8QH6JcC8

Practice 8:
Multiple sequence alignment

https://www.youtube.com/watch?v=WbdsfkzaVqk

Practice 9:
Kyoto Encyclopedia of Genes and Genomes (KEGG): Modules, Network, Genomes, Genes and KEGG analysis tools

https://www.youtube.com/watch?v=CvnmcH7jt1Y

https://www.youtube.com/watch?v=Su5RDSxRsvA

https://www.youtube.com/watch?v=W91YQJuuzV0

Practice 10:
DNA Data Bank of Japan (DDBJ): Sequence Alignment Methods, Predictive Methods Using DNA Sequences.

https://www.youtube.com/watch?v=OoDF_uMGxqU

https://www.youtube.com/watch?v=v9bHE8MfdtU

Practice 11:
Protein Information Resources (PIR)

https://www.youtube.com/watch?v=KJzMtNuqWFE

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

https://www.youtube.com/watch?v=ciD60iJ87vE

https://www.youtube.com/watch?v=hgisJGM5Fho

Practice 13:
Phylogenetic analysis.

https://www.youtube.com/watch?v=encRU80nOHg

Practice 14:
Evolution, elements of phylogeny, methods of phylogenetic analysis

https://www.youtube.com/watch?v=09eD4A_HxVQ&t=5s

Practice 15:
Phylogenetic tree of life, comparison of genetic sequence of organisms

https://www.youtube.com/watch?v=EHO-Q21b-_E

Practice 16:
Phylogenetic analysis tools-Phylip

https://www.youtube.com/watch?v=9QZvran_Lfs

Practice 18:
BLAST: Basic Local Alignment Search Tool

https://www.youtube.com/watch?v=RzC-V67z5LA

Practice 19:
Nucleotide BLAST

https://www.youtube.com/watch?v=TiF_reINXqw

Practice 20:
Protein BLAST

https://www.youtube.com/watch?v=lV-oB0MBUfI

Practice 22:
Sequence Alignment

https://www.youtube.com/watch?v=zBGAtxrJx0M

Practice 23:
MSA using conserved domain and local sequence similarity information

https://www.youtube.com/watch?v=4WH-HmJq_P4

https://www.youtube.com/watch?v=uOOr6XncGdc

Practice 24:
Sequence Alignment: COBALT

https://www.youtube.com/watch?v=9E4BhAVWaNo

Practice 25:
Protein Sequence Alignment

https://www.youtube.com/watch?v=9bCkAsaP_z4

Practice 26:
Nucleotide Sequence Alignment

https://www.youtube.com/watch?v=g9PJEDmoWn4

Practice 27:
Applications of bioinformatics tools in Agriculture

https://www.youtube.com/watch?v=JQixhya1xpw

Applications of bioinformatics tools in Agriculture GPL

Practice 28:
Applications of bioinformatics tools in Medicine

https://www.youtube.com/watch?v=e0LYWrZKQEk

Applications of bioinformatics tools in Medicine GPL

Practice 29:
Applications of bioinformatics tools in Health Industry

https://www.youtube.com/watch?v=rgkku70rZGM

Applications of bioinformatics tools in Health Industry

Practice 30:
Applications of bioinformatics tools in Diary

https://www.youtube.com/watch?v=976cwl5sYJg

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

https://www.youtube.com/watch?v=sKlkWa3nUOM

Practice 33:
Applications of bioinformatics tools in Genomics

https://www.youtube.com/watch?v=sKlkWa3nUOM

Practice 34:
Applications of bioinformatics tools in Transcriptomics

https://www.youtube.com/watch?v=WbJ9OA2vevk

Practice 35:
Applications of bioinformatics tools in Proteomics

https://www.youtube.com/watch?v=8XS0cqxD5XU

Practice 36:
Bioinformatics and Career

https://www.youtube.com/watch?v=1c0BLG2fkJw

Projects:

  1. Genome-wide identification of specific genes in medicinal plants.
  2.  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, […]