construction of substitution matrices blosum blo cks su bstitution m atrix pam
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Construction of Substitution matrices BLOSUM BLO CKS SU BSTITUTION M ATRIX PAM P OINT A CCEPTED M UTATIONS. Substitution matrices - PowerPoint PPT PresentationTRANSCRIPT
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Construction of Substitution matrices
• BLOSUM
• BLOCKS SUBSTITUTION MATRIX
• PAM
• POINT ACCEPTED MUTATIONS
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Substitution matrices
• Substitution matrix contains values proportional to the probability that amino acid A mutates into amino acid B for all pairs of amino acids through a period of evolution
• Substitution matrices are constructed from a large and diverse sample of sequence alignments
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How to construct substitution matrices
• Multiple alignment of well studies gene sequences from different species
• use orthologs: functionally similar
• observed substitutions tend to preserve functions
• minimal gaps
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How to construct substitution matrices ?
• Tabulate substitutions
• A to A: 9867 times
• A to R: 2 times
•A to N: 9 times
• etc….
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How to construct substitution matrices ?
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Construction of Substitution matrices
• BLOSUM
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Construction of Substitution matrices
• BLOSUM
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How to construct substitution matrices ?
Substitution matrix score =
Log Observed mutation rate in alignmentExpected random mutation rate
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How do we find the random mutation rate?
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The random mutation rate
• compute the overall occurrence of an amino acid in a protein database
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The random mutation rate
• compute the overall occurrence of an amino acid in a protein database
http://www.ebi.ac.uk/swissprot/sptr_stats/index.html
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The random mutation rate
Example:
Expected random mutation rate is 1 in 10000 and observed mutation rate of W to R is 1 in 10
Score = log (0.1/0.0001) = log (1000) = +3
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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Calculating BLOSUM62 scores
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PAM matrices
• Point Accepted Mutations
[1 point mutation per 100 amino acids]
• does not take into account different evolutionary rates between conserved and non-conserved regions
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• PAM1 is 1% average change in amino acids
• PAM 250:??
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Why use substitution matrices?????
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Why use substitution matrices?
• Database searches
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Database searching
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Database searching
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Database searching
• Query Sequence; Database sequences
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Database searching: Filtering
• Dynamic programming is computationally expensive
• Apply DP to sequence pairs that are likely to be similar
• find short words: query-database
• DNA 7-28bases (BLAST?)• PROTEIN 3 amino acids (BLAST?)
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BLAST
• Basic Local Alignment Search Tool
• Heuristic method?
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Blast output parameter
E value
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E value
• number of alignments one can expect see by chance.
• Number of alignments having the same or greater score.
• Dependent on size of database and length of query seq.
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