Table of Contents Bioinformatics Biomedical Sciences

Inhoudstafel bioinformatics
1. Introduction
a. What is bioinformatics?
i. ‘-omics’: genomics (functional, structural, comparative),
transcriptomics, preoteomics
ii. Human Genome Project
iii. Ethical issues
b. Computer & applicaitons
i. Hardware
ii. Bits & bytes
iii. Moore’s law
iv. Operating system
v. Applications
vi. User

2. Biological databases
a. Context & history
i. Goal of biological databases
ii. What is a database (DB)?
iii. Flat file DB
iv. Relational DB
v. Some terminology on DBs
vi. Sequence databases: general & spacialized
b. GenBank
i. Sequence information, accession numbers are shared
between NCBI/EMBL-EBI/DDBJ, features, sequence data, FASTA
format
ii. RefSeq
c. Protein databases
i. UniProt

3. Data queries
a. Querying nucleotide sequences at NCBI (genbank)
i. Boolean operators
ii. Boolean algebra
iii. Advanced search
b. GQuery: global cross-database NCBI search
c. Querying uniprot
d. Biomart

4. Genome browers
a. UCSC
i. Genome browser
b. Ensebl

5. Sequence algignment – Part I: pairwise alignment
a. Introduction
i. Similarity vs homology
ii. Mutations