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Sequence Alignment and Phylogeny

Sequence Alignment and Phylogeny. B I O I N F O R M A T I C S | | | | | | | B I O L O G Y - M A T H - S. Dr Peter Smooker, peter.smooker@rmit.edu.au. Uses of alignments. To determine the relationship (ie: distance) between two sequences (pair-wise alignment)

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686 views • 54 slides

Substitution matrices

Substitution matrices. Sequence analysis 2007. Definition. Two-dimensional matrix with score values describing the probability of one amino acid or nucleotide being replaced by another during sequence evolution. Can be more complicated:

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479 views • 45 slides

Measuring the degree of similarity: PAM and blosum Matrix

Measuring the degree of similarity: PAM and blosum Matrix. Lecture 13. Introduction. Measurement of matching Nucleic acid and amino acid substitutions The blosum Matrix The Pam Matrix Appropriate use of blosum and Pam Matrix Measurement of alignment gaps. Measurement of matching.

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689 views • 18 slides

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Pam 1 matrix - PowerPoint PPT Presentation

Sequence Alignment and Phylogeny

Substitution matrices

Measuring the degree of similarity: PAM and blosum Matrix