Course

Unit 1

Introduction: Bioinformatics- Bioinformatics; Components; Different fields in bioinformatics; Omics; Biological Data Acquisition; Types of DNA sequences; RNA sequencing methods; Protein sequencing and structure determination methods; Gene expression data. 

Unit 2

 Databases- Format and Annotation: Conventions for databases indexing and specification of search terms; Common sequence file formats; Files for multiple sequence alignment; Files for structural data; Annotated sequence databases – primary sequence databases; Subsidiary data storage unfinished genomic sequence data, organisms specific databases; Protein sequence and structure databases; List of Gateways, RNAi databases, Data – Access, Retrieval and Submission: Data Access – standard search engines; Data retrieval; Software for data building; Submission of new and revised data. NCBI resource; databases

Unit 3

Sequence alignment- Sequence Similarity Searches: Sequence homology as product of molecular evolution; Sequence similarity searches; Significance of sequence alignment; Sequence alignment; Alignment scores and gap penalties; Measurement of sequence similarity; Similarity and homology. Methods of Sequence Alignment, Graphic similarity comparison; Dot plots; Scoring mutation probability matrices; Sequence similarity searches and alignment tools Heuristic Methods of sequence alignment, FASTA, BLAST and PSI BLAST, Multiple Sequence Alignment, Significance of multiple sequence alignment; Softwares ;Clustal package; Considerations while choosing a MSA software for analysis; Sensitivity and specificity of each software. Methods used to come up with the tree structure, Cladogram, Phylogram, Tools like- Phylip, MEGA. DOMAINS AND MOTIFS: Introduction to motifs and domains, Introduction to signature patterns, Identify patterns, Tools like- Prosite, Pfam, InterPro scan

Unit 4

Visualization tools and genome analysis- Pymol, VMD, Rasmol, Swisspdb viewer. Structure of genome; Anatomy of genomes of virus, prokaryotes, eukaryotes; Human genome Genome Analysis, Whole genome analysis – shotgun sequencing, clone contig; Genomic library; Isolation and microdissection of chromosomes; Hybridisation methods – northern blot, southern blot, western blot; Genome identification Feature based approach – ORF’s; Primer Designing; Vector designing; APE

Unit 5

Introduction, the what and why of NGS– Concepts of Whole Exome Sequencing/Whole Genome Sequencing; Concepts of whole Transcriptome Shotgun Sequencing (WTSS) and RNA-Seq; Introduction to Bacterial Genome Sequencing and Metagenomics; Introduction to Oxford Nanopore read sequencing; Introduction to Galaxy; Case studies

LEARNING OBJECTIVE:

To introduce to the field of bioinformatics via an array of publicly available tools and resources.

COURSE OUTCOME:

After completing the course, students shall be able to

CO1: Define concepts in bioinformatics that could help to solve life science problems 

CO2: Classify the different biological data and relate it to the known databases and formats

CO3: Demonstrate tools for sequence alignment, phylogenetics, characterization, and visualization of biomolecules 

CO4: Analyze, compare and apply basic bioinformatic tools for finding motifs, domains gene/protein homologs, designing primers, identifying mutations.

CO5: Understanding the concepts of NGS and other sequencing techniques. 

REFERENCES:

1. Vittal R.Srinivas, ” BIOINFORMATICS: A MODERN APPROACH”, 2005, ISBN: 978-81-203-2858-7, published by PHI Learning Private Limited, New Delhi.
2. Andreas D.Baxevanis, B.F. Francis Ouellette, “Bioinformatics – A Practical Guide to the Analysis of Genes and Proteins”, Third Edition, 2005-2006, ISBN: 978-81-265-2192-0, published by John Wiley & Sons INC., U.K.
3. Jean-Michel Claverie, Cedric Notredame, “Bioinformatics for Dummies”, 2nd Edition, 2006, ISBN: 978-0-470-08985-9
4. Buermans HP, den Dunnen JT. Next generation sequencing technology: Advances and applications. Biochim Biophys Acta. 2014 Oct;1842(10):1932-1941. doi: 10.1016/j.bbadis.2014.06.015. Epub 2014 Jul 1. PMID: 24995601.
5. Goodwin, S., McPherson, J. & McCombie, W. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17, 333–351 (2016). https://doi.org/10.1038/nrg.2016.49