SEMESTER – V
GE – 1
APMB 357 BIOINFORMATICS (3 credits)
Unit - I
Analysis of DNA and protein sequences – codon distributions, frequency statistics, pattern and motif searches – randomization.
Unit - II
Sequence alignments: Scoring matrices – PAM and BLOSUM – local and global alignment concepts – dynamic programming methodology –
Needleman and Wunsch algorithm, Smith – Waterman algorithm – statistics of alignment score – multiple sequence alignment –
progressive alignment – database searches for homologous sequences – FASTA and BLAST versions.
Unit - III
Evolutionary analysis: distances – clustering methods – rooted and unrooted tree representations – bootstrapping strategies.
Unit - IV
Fragment assembly – genome sequence assembly. Gene finding methods: content and signal methods, gene prediction – analysis and prediction of regulatory regions.
Unit - V
Neural network – concepts and secondary structure prediction – probabilistic models: Markov chain – random walk – hidden Markov models – gene identification and other applications.
Text Books
1. Lesk M.A. (2008) Introduction to Bioinformatics, 3rd International Student Edition, Oxford Publication.
2. Claverie J.M. and Notredame C. (2007) Bioinformatics for Dummies, 2nd Edn. Wiley Publishers.
Reference Books
1. Rastogi S.C., Mendiratta, N. and Rastogi P. (2007) Bioinformatics – Concepts, Skills, Applications, 2nd Edn. Prentice Hall India Publication.
2. Hodgman T.C., French A. and Westhead D.R. (2010) Bios Instant Notes Bioinformatics, Taylor & Francis.
3. Mount D.W. (2005) Bioinformatics: Sequence and Genome analysis, 2nd Edn. Paperback, CBS Publishers.