Introduction to BioinformaticsTuesday, 12 March

Introduction to BioinformaticsThursday, 28 February

How to choose your research group

Mueser TC et al (2010) Virol J 7:359

Origin of DNA replicationCircular, dsDNA

genome

Origin

Origin of DNA replicationCircular, dsDNA

genome

Origin

Bidirectionalinitiation

Origin of DNA replicationCircular, dsDNA

genome

Bidirectionalinitiation

Origin

Elongation

Separation

Origin of DNA replicationOrigin

Origin of DNA replicationOrigin

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Origin of DNA replicationOrigin

+

+

FISFactor for Inversion

Stimulation in Phage Mu

IHFIntegration Host

Factor for lysogeny of Phage Lambda

Origin of DNA replicationOrigin

+

+

How to recognize origin of replication?

Origin of DNA replication

Kaguni (2006) Annu Rev Microbiol 60:351-371.

Fuller et al (1984) Cell 38:889-900.

DnaA binding site

Origin of DNA replication

Kaguni (2006) Annu Rev Microbiol 60:351-371.

Fuller et al (1984) Cell 38:889-900.

DnaA binding site

R1 TTATCCACAR2 TTATACACAR3 TTATCCAAAR4 TTATCCACA

Origin of DNA replication

Fuller et al (1984) Cell 38:889-900.

Find it myself

R1 TTATCCACAR2 TTATACACAR3 TTATCCAAAR4 TTATCCACA

Origin of DNA replicationAlgorithm

* Search genome sequence for DnaA-binding sites - TTAT[CA]CACA - One mismatch? - Use MATCHES-OF-PATTERN

* Sort sites by coordinate - Use SORT

* Add context - Loop through sites - JOIN site information with CONTEXT-OF

* Look for clusters - ???

Apply to all phage genomes

* Make problem tangible

Morals of the Story

* Experiment

* Package procedure

Annotation of genes

T4p051

T4p104

T4p120

T4p044

T4p113