Course Contents

THEORY: Introduction to BI: What is BI; history of BI; Uses of BI (Protein, Gene); Basic principles of computing in bioinformatics: Basic acquisition and database: DDBJ, NCBI and EMBL Short introduction to protein: amino acids, protein sequence, structures and functions Retrieving the DNA sequence from database; Computing the sequence Identifying restriction sites; Computing physicochemical parameters of proteins (eg. PROTPARAM). Computing the optimal alignment between two or more DNA sequences PRIMER designing for PCR (PRIMER3+ and OLIGO-CALC etc.) Retrieving protein sequences from database (FASTA): Alignment of protein\ nucleotide sequences (BLAST, CLUSTALW); Predicting elements of secondary structure of proteins (eg. APSSP, JPRED); Retrieval, understanding and predicting 3D structure of protein from sequence; PTMs (eg NETPHOS, YINOYANG etc.) Enzyme classification: retrieval databases. Predicting elements of DNA/RNA secondary structure; (RNA CENTRAL FOR DATABASE (RANA FOLDING FOR STRUCTURE) Short introduction to DNA/RNA: structure, Genetic Code; Analyzing the DNA/RNA sequence by the use of BI tools PRACTICALS 1. Retrieval of FASTA sequence 2. Determination of proteins physical and chemical parameters 3. Finding similar sequences for protein and DNA 4. Multiple alignment 5. Predicting proteins secondary structure 6. Predicting RNA secondary structure 7. Predicting protein PTM (Expasy tools) 10. Primer design 11. SNPs

Course Learning Outcomes

• An introduction to bioinformatics with a focus on fundamental bioinformatics problems, • Information on the tools used to compute solutions to those problems, and the theory upon which those tools are based.