'Pam matrices' diaporamas de présentation

Sequence Analysis

Sequence Analysis. Sequence Analysis: Outline. Why do we compare sequences? Sequence comparison: from qualitative to quantitative methods Deterministic methods: Dynamic programming Heuristic methods: BLAST Multiple Sequence Alignment. Sequence Analysis. Why do we compare sequences?

1.18k views • 83 slides

Sequence Analysis

Sequence Analysis. Sequence Analysis: Outline. Why do we compare sequences? Sequence comparison: from qualitative to quantitative methods Deterministic methods: Dynamic programming Heuristic methods: BLAST Multiple Sequence Alignment. Sequence Analysis. Why do we compare sequences?

835 views • 83 slides

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)

686 views • 54 slides

Sequence similarity search II Searching for remote homologies

Sequence similarity search II Searching for remote homologies. (How) can we decide if two sequences have the same function?. Homolog = come from a common origin => have the same function. Homologous proteins = come from a common origin => have the same function.

444 views • 44 slides

462 views • 41 slides

Heuristic Approaches for Sequence Alignments

Heuristic Approaches for Sequence Alignments. Outline. Sequence Alignment Database Search FASTA BLAST. Sequence Alignment. Dynamic Programming (give optimal solution(s)) Needleman-Wunsch (Global Alignment) Smith-Waterman (Local Alignment) Heuristics (give approximate solution(s))

576 views • 37 slides

377 views • 37 slides

Sequence Alignment III Lecture #4

Sequence Alignment III Lecture #4. Background Readings : The second chapter (pages 12-45) in the text book, Biological Sequence Analysis , Durbin et al., 2001. Chapter 3 in Introduction to Computational Molecular Biology , Setubal and Meidanis, 1997.

413 views • 32 slides

Substitution Matrices and Alignment Statistics

Substitution Matrices and Alignment Statistics. BMI/CS 776 www.biostat.wisc.edu/~craven/776.html Mark Craven craven@biostat.wisc.edu February 2002. Substitution Matrices. two popular sets of matrices for protein sequences PAM matrices [Dayhoff et al., 1978]

276 views • 18 slides

Alignment III PAM Matrices

Alignment III PAM Matrices. PAM250 scoring matrix. 0. + 3. + ( -3 ). + 1. Scoring Matrices. S = [s ij ] gives score of aligning character i with character j for every pair i, j. S T P P C T C A. = 1. Scoring with a matrix.

201 views • 16 slides