'Blosum matrices' diaporamas de présentation

Evolution and Scoring Rules

Evolution and Scoring Rules. Example Score = 5 x (# matches) + (-4) x (# mismatches) + + (-7) x (total length of all gaps) Example Score = 5 x (# matches) + (-4) x (# mismatches) + + (-5) x (# gap openings) + (-2) x (total length of all gaps). Scoring Matrices.

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Chapter 2 Data Searches and Pairwise Alignments

Chapter 2 Data Searches and Pairwise Alignments. ?????????? ??? 2004/03/08. Introduction. What is the difference between acctga and agcta?. a c c t g a a g c t g a a g c t - a. Nomenclature. 2.1 Dot Plots. 2.2 Simple Alignments. No gap. mutation (substitution): common insertion

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Basics of Sequence Alignment and Weight Matrices and DOT Plot

Basics of Sequence Alignment and Weight Matrices and DOT Plot. G P S Raghava Email: raghava@imtech.res.in Web: http://imtech.res.in/raghava/. Importance of Sequence Comparison. Protein Structure Prediction Similar sequence have similar structure & function Phylogenetic Tree

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Basics of Sequence Alignment and Weight Matrices and DOT Plot

Basics of Sequence Alignment and Weight Matrices and DOT Plot. G P S Raghava Email: raghava@imtech.res.in Web: http://imtech.res.in/raghava/. Importance of Sequence Comparison. Protein Structure Prediction Similar sequence have similar structure & function Phylogenetic Tree

393 views • 35 slides

Alignment and Algorithms

Alignment and Algorithms. Scoring Matrices: models of evolution Dynamic Program: speed Pairwise Sequence Alignment, variants Significance Pattern recognition, Hidden Markov Models (HMM) Multiple Sequence Alignment (MSA) Protein families Structure features. Scoring Models and Evolution.

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Pairwise Sequence Alignment

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Comparing Protein Sequences

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Alignment IV BLOSUM Matrices

Alignment IV BLOSUM Matrices. BLOSUM matrices. Blo cks Su bstitution M atrix. Scores for each position are obtained frequencies of substitutions in blocks of local alignments of protein sequences [Henikoff & Henikoff92].

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Blosum matrices Morten Nielsen Department of systems biology, DTU

Blosum matrices Morten Nielsen Department of systems biology, DTU. Outline. Alignment scoring matrices What is a BLOSUM50 matrix and how is it different from a BLOSUM80 matrix? What are Blosum matrices good for? Sequence alignment Infer properties from one protein to another.

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