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BIOINFORMATICS
The objectives of this course are to provide theory and practical experience of the use of common computational tools and databases which facilitate investigation of molecular biology and evolution-related concepts.
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.
