Genome organization and Bioinformatics BI420 – Introduction to Bioinformatics Genome organization and Bioinformatics Gabor T. Marth Department of Biology, Boston College marth@bc.edu

The animal cell

DNA – the carrier of the genetic code

DNA organization – chromosomes

DNA organization – mitochondria

Translation of genetic information

Gene organization

mRNA splicing – alternative splicing

Gene expression

Protein structure

RNA structure

DNA evolution

Mechanisms of molecular evolution

Evolution of chromosome organization

Evolution of gene structure

Evolution of DNA sequence

Genetic variations

1. DNA sequencing informatics

2. Gene prediction, genome annotation

De novo gene prediction

Repeat masking

3. Similarity searching

4. Gene localization – genetic mapping

Genetic mapping

Genetic mapping 0.4 cm 1.3 cm 0.7 cm 0.4 Mb 0.7 Mb 0.3 Mb

5. Polymorphism discovery and analysis look at multiple sequences from the same genome region use base quality values to decide if mismatches are true polymorphisms or sequencing errors

6. Gene function – expression analysis

7. Evolutionary analysis – phylogenetics

Gene evolution

Genome evolution

8. Protein structure prediction + computational predictions based on measurements

9. RNA structure prediction