Bioinformatics – Third Year (B.Sc. Microbiology)

BSc General Microbiology / By

Third Year (B.Sc. Microbiology)

Course Title :Bioinformatics
Course No :MB 304 (Elective II)
Nature of the Course :Theory
Full Marks :50
Pass Marks :17.5
Year :Third( 3rd)
Total Lecture Hours :75

Course Objectives

After completion of the course, the students will be able to:

  • understand the principles and applications of it in microbiological research

Course Contents of bioinformatics

S.NTopic / ChapterLecture hours
1History, Scope and Importance of Bioinformatics


Definition, contribution, aims, tasks , applications , challenges and opportunities in bioinformatics		5hrs
2Internet, World Wide Web and NCBI in Bioinformatics


Computer programs and operating systems for bioinformatics, world wide web pages and websites,
browsers, EMBnet and SRS, Sequence retrieval system, NCBI, Entrez, Data model, basic sites of
bioinformatics		5hrs
3DNA and Protein Sequencing and Analysis


Genomics and proteomics, approaches to genome sequencing, genome mapping, DNA sequencing, ORF,
CDS, determining sequence of a clone, expressed sequence tags, protein sequencing, determination of
protein structure, gene and protein expression analysis, gene finding databases and accession sites,
capturing expression profile, human genome project, benefits of genome research		15hrs
4Databases, Tools and Their Uses


Definition, importance of databases, types of databases, classification, database entries, sequence
formats, database record, database management system, relational database management system,
structured query language, data mining and knowledge discovery, nucleic acid sequence databases
(EMBL, DDBJ, genebank, GSDB, Ensembl, specialized genomic resources, protein sequence databases,
PIR databases, SWISS-PROT, TrEMBL, NRL-3D, Structure classification database (SCOP, CATH, DALI, CE,
NDB, CSD, BMRB, 3Dee, FSSP, MMDB, CDD, Rasmol database), secondary databases (PROSITE, PRINTS,
BLOCKS, HMMs, IDENTIFY, KEGG, MEDLINE databases), Specialized analysis packages (GCG package,
EGCG package, staden package, lasergene package, sequencher package, vector NTI package,
Macvector package), DALI program, uses of databases		15 hrs
5Sequence Alignment


Algorithm, genetic algorithm, goals and types of alignment, study of similarities, high and low scoring
matches, scoring mutations, deletions and substitutions, sequence alignment methods (dot matrix,
dynamic programming, k-tuple, FASTA, BLAST, multiple sequence alignment, automatic alignmentCLUSTAL, CINEMA), algorithms for identifying domains within a protein structure, algorithms for
structural comparisons, sequence search		15hrs
6Predictive Methods Using DNA and Protein Sequences


Gene prediction strategies, prediction of RNA secondary structures, gene prediction programs, protein
prediction strategies and methods, prediction of secondary structure of protein, comparative modeling,
threading, protein function prediction, protein prediction programs, molecular visualization		10hrs
7Homology, Phylogeny, Evolutionary Trees and Pharmainformatics


Definition of homology and similarity, orthologs, paralogs, xenologs, study of orthologous and
paralogous proteins, modular proteins, phylogeny and relationships, evolutionary tree, approaches used
in phylogenetic analysis, steps in phylogenetic analysis, phylogenetic trees, tree building methods,
molecular approaches to phylogeny, phylogenetic analysis databases, definition of pharmainformatics,
chemical libraries, search programs, docking algorithms, active site analysis, QSAR		10 hrs
Total Lecture hours75hrs

Recommended Readings

Text Books

  • Ignacimuthu S. Basic Bioinformatics. Alpha Science International Ltd, UK
  • Campbell AM and Heyer LJ (2007). Discovering Genomics, Proteomics and Bioinformatics (2nd
    Edition). Benjamin Cummings; CSH Press, Newyork .

Reference Books