Course

Biological Data Acquisition: The form of biological information. Retrieval methods for DNA sequence, protein sequence and protein structure information; 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; Data – Access, Retrieval and Submission: Standard search engines; Data retrieval tools – Entrez, DBGET and SRS; Submission of (new and revised) data; Sequence Similarity Searches: Local versus global. Distance metrics. Similarity and homology. Scoring matrices. Dynamic programming algorithms, Needleman-wunsch and Smith-waterman. Heuristic Methods of sequence alignment, FASTA, BLAST and PSI BLAST. Multiple Sequence Alignment and software tools for pairwise and multiple sequence alignment; Genome Analysis:  Whole genome analysis, existing software tools; Genome Annotation and Gene Prediction; ORF finding; Phylogenetic Analysis: Comparative genomics, orthologs, paralogs. Methods of phylogenetic analysis: UPGMA, WPGMA,  neighbour joining method, Fitch/Margoliash method,  Character Based Methods.

1. Bioinformatics: Databases and Systems, by Stanley I. Letovsky
2. Bioinformatics Databases: Design, Implementation, and Usage (Chapman & Hall/ CRC Mathematical Biology & Medicine), by SorinDraghici
3. Data base annotation in molecular biology, principles and practices, Arthur M.Lesk
4. Current topics in computational molecular biology, Tao, Jiang, Ying Xu, Michael Q.Zang