Introductory Bioinformatics for BSc Biotechnology and BSc Microbiology
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
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