OBT552 Basics of Bioinformatics Syllabus:

OBT552 Basics of Bioinformatics Syllabus – Anna University Regulation 2017

UNIT I BIOLOGICAL DATA ACQUISITION

The form of biological information. Retrieval methods for DNA sequence, protein sequence and protein structure information

UNIT II DATABASES

Format and Annotation: Conventions for database indexing and specification of search terms, Common sequence file formats. Annotated sequence databases – primary sequence databases, protein sequence and structure databases, Organism specific databases

UNIT III DATA PROCESSING

Data – Access, Retrieval and Submission: Standard search engines; Data retrieval tools – Entrez, DBGET and SRS; Submission of (new and revised) data; Sequence Similarity Searches: Localversus global. Distance metrics. Similarity and homology. Scoring matrices.

UNIT IV METHODS OF ANALYSIS

Dynamic programming algorithms, Needleman-wunsch and Smith-waterman. Heuristic Methods of sequence alignment, FASTA , and PSI BLAST. Multiple Sequence Alignment and software tools for pairwise and multiple sequence alignment

UNIT V APPLICATIONS

Genome Annotation and Gene Prediction; ORF finding; Phylogenetic Analysis : Comparative genomics, orthologs, paralogs. Genome analysis – Genome annotation

TEXT BOOKS:

1. Introduction to Bioinformatics by Arthur K. Lesk , Oxford University Press.
2. Algorithms on Strings, Trees and Sequences by Dan Gusfield, Cambridge University Press.
3. Biological Sequence Analysis Probabilistic Models of proteins and nucleic acids by Durbin, S.Eddy, A.Krogh, G.Mitchison.
4. Bioinformatics Sequence and Genome Analysis by David W. Mount, Cold Spring Harbor Laboratory Press.
5. Beginning Perl for Bioinformatics: An introduction to Perl for Biologists by James Tindall, O‟Reilley Media.

REFERENCE:

1. Bioinformatics The Machine Learning Approach by Pierre Baldi and Soren Brunak.