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CSE182-L4: Keyword matching

CSE182-L4: Keyword matching

CSE182-L4: Keyword matching. Backward scoring. Defin S b [i,j] : Best scoring alignment of the suffixes s[i+1..n] and t[j+1..m] Q: What is the score of the best alignment of the two strings s and t? HW: Write the recurrences for S b. Forward/Backward computations. j. m. 1.

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725 views • 60 slides
CSE182-L4: Keyword matching

CSE182-L4: Keyword matching

CSE182-L4: Keyword matching. Backward scoring. Defin S b [i,j] : Best scoring alignment of the suffixes s[i+1..n] and t[j+1..m] Q: What is the score of the best alignment of the two strings s and t? HW: Write the recurrences for S b. Forward/Backward computations. j. m. 1.

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607 views • 60 slides
Heuristic Approaches for Sequence Alignments

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))

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575 views • 37 slides
CSE182-L5: Scoring matrices Dictionary Matching

CSE182-L5: Scoring matrices Dictionary Matching

CSE182-L5: Scoring matrices Dictionary Matching. Silly Quiz. PAM 1 distance. Two sequences are 1 PAM apart if they differ in 1 % of the residues. 1% mismatch. PAM 1 (a,b) = Pr[residue a substitutes residue b, when the sequences are 1 PAM apart]. PAM 1. Generating Higher PAMs.

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550 views • 32 slides
CSE182-L5: Scoring matrices Dictionary Matching

CSE182-L5: Scoring matrices Dictionary Matching

CSE182-L5: Scoring matrices Dictionary Matching. Silly Quiz. PAM 1 distance. Two sequences are 1 PAM apart if they differ in 1 % of the residues. 1% mismatch. PAM 1 (a,b) = Pr[residue a substitutes residue b, when the sequences are 1 PAM apart]. PAM 1. Generating Higher PAMs.

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345 views • 32 slides
CSE182-L4: Scoring matrices, Dictionary Matching

CSE182-L4: Scoring matrices, Dictionary Matching

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404 views • 30 slides
CSE182-L4: Database filtering

CSE182-L4: Database filtering

CSE182-L4: Database filtering. Summary (through lecture 3). A2 is online We considered the basics of sequence alignment Opt score computation Reconstructing alignments Local alignments Affine gap costs Space saving measures

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304 views • 30 slides
CSE182-L4: Scoring matrices, Dictionary Matching

CSE182-L4: Scoring matrices, Dictionary Matching

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323 views • 30 slides

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