Introduction to Bioinformatics Tuesday, 12 March.

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Presentation transcript:

Introduction to Bioinformatics Tuesday, 12 March

Introduction to Bioinformatics Thursday, 28 February

How to choose your research group Mueser TC et al (2010) Virol J 7:359

Origin of DNA replication Circular, dsDNA genome Origin

Origin of DNA replication Circular, dsDNA genome Origin Bidirectional initiation

Origin of DNA replication Circular, dsDNA genome Bidirectional initiation Origin Elongation Separation

Origin of DNA replication Origin

Origin of DNA replication Origin +

Origin of DNA replication Origin + + FIS Factor for Inversion Stimulation in Phage Mu IHF Integration Host Factor for lysogeny of Phage Lambda

Origin of DNA replication Origin + + How to recognize origin of replication?

Origin of DNA replication Kaguni (2006) Annu Rev Microbiol 60: Fuller et al (1984) Cell 38: DnaA binding site

Origin of DNA replication Kaguni (2006) Annu Rev Microbiol 60: Fuller et al (1984) Cell 38: DnaA binding site R1 TTATCCACA R2 TTATACACA R3 TTATCCAAA R4 TTATCCACA

Origin of DNA replication Fuller et al (1984) Cell 38: Find it myself R1 TTATCCACA R2 TTATACACA R3 TTATCCAAA R4 TTATCCACA

Origin of DNA replication Algorithm * 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