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Introduction to Bioinformatics Tuesday, 12 March
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Introduction to Bioinformatics Thursday, 28 February
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How to choose your research group Mueser TC et al (2010) Virol J 7:359
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Origin of DNA replication Circular, dsDNA genome Origin
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Origin of DNA replication Circular, dsDNA genome Origin Bidirectional initiation
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Origin of DNA replication Circular, dsDNA genome Bidirectional initiation Origin Elongation Separation
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Origin of DNA replication Origin
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Origin of DNA replication Origin +
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Origin of DNA replication Origin + + FIS Factor for Inversion Stimulation in Phage Mu IHF Integration Host Factor for lysogeny of Phage Lambda
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Origin of DNA replication Origin + + How to recognize origin of replication?
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Origin of DNA replication Kaguni (2006) Annu Rev Microbiol 60:351-371. Fuller et al (1984) Cell 38:889-900. DnaA binding site
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Origin of DNA replication Kaguni (2006) Annu Rev Microbiol 60:351-371. Fuller et al (1984) Cell 38:889-900. DnaA binding site R1 TTATCCACA R2 TTATACACA R3 TTATCCAAA R4 TTATCCACA
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Origin of DNA replication Fuller et al (1984) Cell 38:889-900. Find it myself R1 TTATCCACA R2 TTATACACA R3 TTATCCAAA R4 TTATCCACA
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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
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* Make problem tangible Morals of the Story * Experiment * Package procedure
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Annotation of genes T4p051 T4p104 T4p120 T4p044 T4p113
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