SCHOOL OF BIOTECHNOLOGY, CHEMICAL & BIOMEDICAL ENGINEERING

Vellore 632 014, Tamil Nadu, India.

Biological Data bases Version No. Course Prerequisites Objectives: LTPC: 3 0 0 3

Expected Outcome:

1.0.0 Biochemistry To give the students a basic knowledge of the available biological databases available on the web. The main objective to the make the students understand the use of all kinds of nucleotide and protein databases and the best use of it through out their course. This helps the students to acquire informations from the databases according to their area of interest. 1. The students will be able to search and analyze nucleotide and protein data from various databases. 2. The students will get a wide knowledge of model organisms and to browse genome databases to retrieve useful informations which will be helpful for their research work.

Unit No. 1 Introduction to Data Bases Number of hours: 9 Internet Basics, DNA sequencing, sequencing, submission of sequences to the database, sequence accuracy, computer storage of sequences, sequence formats, conversion of one sequence into another. Unit No. 2 Primary Data Bases Number of hours: 9 Primary nucleotide sequence database: NCBI, EMBL, DDBJ. Primary Protein sequence databases: UNIPROT, SWISS-PROT, NBRF-PIR. Unit No. 3 Secondary Data Bases Number of hours: 9 Secondary nucleotide database: Repetitive sequence database (RSDB), regulatory sequence databasesTRANSFAC, plant cis-acting regulatory DNA elements (PLACE) database, the exon-intron database (EID), single exonic genes from eukaryotes (SEGE). Secondary protein databases: Pfam, PRINTS, ProDom, SMART, BLOCKS, InterPro, ProtoNet, ProtoMap, Unit No. 4 Structural databases Number of hours: 9 Introduction to structures. Macromolecular databases: PDB, MMDB, NCI, MSD, Mod Base. Small molecular database: NCI, CSD-Cambridge small- molecular crystal structure data bank. Unit No. 5 Other Data Bases Number of hours: 9 Specialized genome data banks: ENSEMBL browser, Mouse, Arabidopsis, Caenorhabditis, YGD, Viral genomes, Bacterial genomes, TIGR, Metabolic pathway databases: KEGG, BIND, DIP. Text Books Baxevanis A., Ouellette F.B.F. (Eds.) Bioinformatics: a practical guide to the analysis of genes and proteins. John Wiley and Sons, New York (1998). References 1. Westhead, D.R., J.H. Parish and R. M. Twyman. Introduction to Bioinformatics, Viva Books 2003. 2. Attwood T. K., D. J. Parry-Smith, Introduction to Bioinformatics, Prentice-Hall. 3. David W Mount Bioinformatics Sequence and genome analysis Mode of Announced / Unannounced Quiz / tests, Assignments and Written Examination Evaluation Recommended 13th November 2008 by the Board of Studies on Date of Approval by the Academic Council

Proceedings of the 16th Academic Council held on 25.11.2008