Programming for Bioinformatics- Lab First Semester Syllabus for MSc Bioinformatics
COURSE NAME: Programming for Bioinformatics- Lab
COURSE CODE: BIF487
PROGRAM: MSc Bioinformatics
Introduction to Matlab, Matrix calculations, Functions. ENTREZ,NCBI,Genomicdatabases,Organism specific databases, BLAST, FASTA, Phylip, Pymol, Prosite. Exploring NCBI Resouces, GenBank; Moleculardatabases (sequence databases - nucleotides, proteins, structures, genes, expression, taxonomy; Marker databases – dbSNP, dbSTS, dbEST, Unigene),genomes and maps, tools (Entrez, BLAST, nucleotide sequence analysis, protein sequence analysis, 3-D structure display and similarity searching), Literature Databases (PubMed, PubMedCentral, OMIM, Books, Citation Matcher), research at NCBI, education, FTP site. Searching and retrieval of nucleotide sequences from GenBank database, Retrieval of protein sequences from “SWISS-PROT” database. Searching and retrieving the protein structure data using Entrez and protein viewing softwares. Database homology search of a nucleotide sequence using Blastn, Retrieval of related sequences in a given format. Modeling solvers – Euler, Runge-Kutta, numerical integration.