Applied Bioinformatics Course

Outline

1. Getting started with applied bioinformatics
   1. An overview of bioinformatics
   2. The basis of molecular biology
2. Bioinformatics resources over the Internet
   1. International bioinformatics centers (NCBI, EBI, ExPASy, RSCB)
   2. Literature references (PubMed, PubMed Central, Online books, bioinformatics courses, tutorials)
   3. Databases of molecular biology (Genome, sequence, function structure databases)
   4. Bioinformatics tools (programs, packages, online web servers)
3. Database query
   1. Database query with the NCBI Entrez system
   2. Database query with the EBI SRS platform
   3. Database query with the MRS platform
4. DNA and protein sequence analysis
   1. Sequence alignment and dotplot
   2. Protein sequence analysis
   3. DNA sequence analysis
   4. Database similarity search (BLAST, FASTA)
   5. Phylogenic analysis and tree construction
5. Molecular modeling
   1. Molecular graphics and visualization
   2. Molecular modeling and structure prediction
6. Projects
   1. Sequence analysis of Pisum sativum post-floral specific gene
   2. MDR - Gene prediction and dotplot analysis of fugu multi-drug resistance gene
   3. Seqeunce, structure and function analysis the bar-headed goose hemoglobin
   4. CEA - Protein engineering of carcinoembryonic antigen
   5. Structure comparison of spider toxins and prediction of antifungal peptide
   6. Sequence and structure comparison of human metallothioneins
   7. Systematic analysis of the Arabidopsis transcription factor family of Squamosa-promoter binding protein