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BIOINFORMATICS
This course will enable the student to Master bioinformatics tools and databases analyze biological data effectively, explore applications in genomics, proteomics, and beyond and apply knowledge to solve complex biological problems
Bioinformatics basics: Computers in biology and medicine; Introduction to Unix and Linux systems and basic commands; Database concepts; Protein and nucleic acid databases; Structural databases; Biological XML DTD’s; pattern matching algorithm basics; databases and search tools: biological background for sequence analysis; Identification of protein sequence from DNA sequence; searching of databases similar sequence; NCBI; publicly available tools; resources at EBI; resources on web; database mining tools
DNA sequence analysis: gene bank sequence database; submitting DNA sequences to databases and database searching; sequence alignment; pairwise alignment techniques; motif discovery and gene prediction; local structural variants of DNA, their relevance in molecular level processes, and their identification; assembly of data from genome sequencing
Multiple sequence analysis; multiple sequence alignment; flexible sequence similarity searching with the FASTA3 program package; use of CLUSTALW and CLUSTALX for multiple sequence alignment; submitting DNA protein sequence to databases: where and how to submit, SEQUIN, genome centres; submitting aligned sets of sequences, updating submitted sequences, methods of phylogenetic analysis.
Protein modelling: introduction; force field methods; energy, buried and exposed residues; side chains and neighbours; fixed regions; hydrogen bonds; mapping properties onto surfaces; fitting monomers; RMS fit of conformers; assigning secondary structures; sequence alignment- methods, evaluation, scoring; protein completion: backbone construction and side chain addition; small peptide methodology; software accessibility; building peptides; protein displays; substructure manipulations, annealing.
Protein structure prediction: protein folding and model generation; secondary structure prediction; analyzing secondary structures; protein loop searching; loop generating methods; homology modelling: potential applications, description, methodology, homologous sequence identification; align structures, align model sequence; construction of variable and conserved regions; threading techniques; topology fingerprint approach for prediction; evaluation of alternate models; structure prediction on a mystery sequence; structure aided sequence techniques of structure prediction; structural profiles, alignment algorithms, mutation tables, prediction, validation, sequence based methods of structure prediction, prediction using inverse folding, fold prediction; significance analysis, scoring techniques, sequence-sequence scoring; protein function prediction; elements of in silico drug design;Virtual library: Searching PubMed, current content, science citation index and current awareness services, electronic journals, grants and funding information
Lesk, A. M. (2002). Introduction to Bioinformatics. Oxford: Oxford University Press.
• Mount, D. W. (2001). Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
• Baxevanis, A. D., & Ouellette, B. F. (2001). Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins. New York: Wiley-Interscience.
Pevsner, J. (2015). Bioinformatics and Functional Genomics. Hoboken, NJ.: Wiley-Blackwell.
• Bourne, P. E., & Gu, J. (2009). Structural Bioinformatics. Hoboken, NJ: Wiley-Liss.
• Lesk, A. M. (2004). Introduction to Protein Science: Architecture, Function, and Genomics. Oxford: Oxford University Press.
