Course

PART 1: INTRODUCTION

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.

PART 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 databses; 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

PART 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; Hash tables; 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.

PART 4: VISUALISATION 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

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