Syllabus of Jawaharlal Nehru University MSc Biotechnology - BT513 - Computational Biology-I

Credits: 2

Biological Sequence Databases:

Overview of various primary and secondary databases that deal with protein and nucleic acid sequences. Databases to be covered in detail are GenBank, EMBL, DDBJ, SwissProt, PIR, and MIPS for primary sequences. Various specialized databases like TIGR, Hovergen, TAIR, PlasmoDB, ECDC etc., will also be discussed. Preliminary ideas of query and analysis of sequence information.

Sequence Comparison Methods:

Method for the comparison of two sequences viz., Dot matrix plots, Needleman-Wusch & Smith-Waterman algorithms. Analysis of computational complexities and the relative merits and demerits of each method. Theory of scoring matrices and their use for sequence comparison.

Database Search Algorithms:

Methods for searching sequence databases like FASTA and BLAST algorithms. Statistical analysis and evaluation of BLAST results.

Pattern Recognition Methods in Sequence Analysis:

Concept of a sequence pattern, regular expression based patterns. The use of pattern databases like PROSITE and PRINTS. Concept of position specific weight matrices and their use in sequence analysis. Theory of profiles and their use with special reference to PSIBLAst. Markov chains and Markov models and their use in gene finding. Concept of HMMS, the forward-backward and the Viterbi algorithm. The Baum-Welch algorithm for training a HMM. Use of profile HMM for protein family classification.