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C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)

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Presentation on theme: "C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)"— Presentation transcript:

1 C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)

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4 Protein main-chain and side-chain ‘R’ designates the side-chain

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6 charge

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8 (cysteine bridge)

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10 VHLTPEEKSAVTALWGKVNVDE VGGEALGRLLVVYPWTQRFFE SFGDLSTPDAVMGNPKVKAHG KKVLGAFSDGLAHLDNLKGTFA TLSELHCDKLHVDPENFRLLGN VLVCVLAHHFGKEFTPPVQAAY QKVVAGVANALAHKYH PRIMARY STRUCTURE (amino acid sequence) QUATERNARY STRUCTURE (oligomers) SECONDARY STRUCTURE (helices, strands) TERTIARY STRUCTURE (fold) Protein structure hierarchical levels

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16 Compared to preceding plot, RMSD is better able to pin-point relationships between more divergent sequences (RMSD stays relatively small for a longer time as compared to PAM distance). Note that the spread around RMSD is larger

17 Structural superpositioning

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