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Sequence analysis course Lecture 8 Sequence databank searching 1.

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Presentation on theme: "Sequence analysis course Lecture 8 Sequence databank searching 1."— Presentation transcript:

1 Sequence analysis course Lecture 8 Sequence databank searching 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 (cystein 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

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