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