BB410: Bioinformatics-I Lab

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Bioinformatics basics: Searching PubMed, current content, science citation index and current awareness services, electronic journals, grants and funding information. 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.

BLAST: sequence alignment- methods, evaluation, scoring;

Use of various primer designing and restriction site prediction tools. Use of miRNA prediction, designing and target prediction 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 (GRAIL, Genscan, Glimmer); 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.

Text/References :

  • Lesk, M. (2002). Introduction to Bioinformatics. Oxford: Oxford University Press.
  • Mount, D. W. (2001). Bioinformatics: Sequence and Genome Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  • Baxevanis, D., & Ouellette, B. F. (2001). Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins. New York: Wiley-Interscience.
  • Pevsner, (2015). Bioinformatics and Functional Genomics. Hoboken, NJ.: Wiley- Blackwell.
  • Bourne, E., & Gu, J. (2009). Structural Bioinformatics. Hoboken, NJ: Wiley-Liss.
  • Lesk, M. (2004). Introduction to Protein Science: Architecture, Function, and Genomics. Oxford: Oxford University Press.