This is a textbook that accompanies a master's course Introduction to Bioinformatics tought by Blaž Zupan and Tomaž Curk and assited by Pavlin Poličar and Martin Špendl at University of Ljubljana.
main.tex: front matter
c-molbio.tex: Introduction to Molecular Biology
- Overview of concepts of life, cells, proteins, amino acids, and metabolism.
- Sets up key questions and introduces the central dogma as the unifying framework.
c-history.tex: Central Dogma of Molecular Biology
- Explains DNA→RNA→Protein information flow and why it matters.
- In short, revies history of discoveries that led to modern molecular biology.
c-genome.tex: Genomes and Some Simple Sequence Patterns
- Introduces DNA sequences and some simple methods to assess their basic statistical properties.
- Uses viral genomes to illustrate practical mining sequence features with Python programming.
c-genes.tex: Where Are the Genes?
- Covers reading frames, gene structure, ORFs, and gene prediction basics.
- Compares simple statistical models to real gene architectures and discusses scoring and evaluation.
- Introduces permutation-based analysis.
c-alignment-m.tex: Sequence Alignment Methods
- Introduces alignment scoring, dynamic programming, and algorithms for global and local alignment.
- Extends to alignment with affine gap penalties and multiple sequence alignment.
- Discusses protein-specific scoring and inference of scoring tables.
c-alignment-t.tex: Sequence Alignment Tools
- Discusses about various applications of alignment tools.
- Introduces BLAST and CLUSTAL and provides basic understanding of methods behind these techniques.
- Shows some typical examples of use.
split-to-chapters.py splits main.pdf to chapters, creatings one pdf file for each chapter.
copy-to-server is a bash script that copies pdfs of each chapter to the file server