CSE 469 BIO-INFORMATICS
3 Hours/Week, 3 Credits
Cell concept: Structural organization of plant and animal cells, nucleus, cell membrane and cell wall. Cell division: Introducing chromosome, Mitosis, Meiosis and production of haploid/diploid cell. Nucleic acids: Structure and properties of different forms of DNA and RNA; DNA replication. Proteins: Structure and classification, Central dogma of molecular biology. Genetic code: A brief account. Genetics: Mendel's laws of inheritance, Organization of genetic material of prokaryotes and eukaryotes, C-Value paradox, repetitive DNA, structure of chromatin - euchromatin and heterochromatin, chromosome organization and banding patterns, structure of gene - intron, exon and their relationships, overlapping gene, regulatory sequence (lac operon), Molecular mechanism of general recombination, gene conversion, Evolution and types of mutation, molecular mechanisms of mutation, site-directed mutagenesis, transposons in mutation. Introduction to Bioinformatics: Definition and History of Bioinformatics, Human Genome Project, Internet and Bioinformatics, Applications of Bioinformatics Sequence alignment: Dynamic programming. Global versus local. Scoring matrices. The Blast family of programs. Significance of alignments, Aligning more than two sequences. Genomes alignment. Structure-based alignment. Hidden Markov Models in Bioinformatics: Definition and applications in Bioinformatics. Examples of the Viterbi, the Forward and the Backward algorithms. Parameter estimation for HMMs. Trees: The Phylogeny problem. Distance methods, parsimony, bootstrap. Stationary Markov processes. Rate matrices. Maximum likelihood. Felsenstein's post-order traversal. Finding regulatory elements: Finding regulatory elements in aligned and unaligned sequences. Gibbs sampling. Introduction to microarray data analysis: Steady state and time series microarray data. From microarray data to biological networks. Identifying regulatory elements using microarray data. Pi calculus: Description of biological networks; stochastic Pi calculus, Gillespie algorithm.