Ch06_MultAlign

Ch06_MultAlign - An Introduction to Bioinformatics...

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    www.bioalgorithms.info An Introduction to Bioinformatics Algorithms Multiple Alignment
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline Dynamic Programming in 3-D Progressive Alignment Profile Progressive Alignment (ClustalW) Scoring Multiple Alignments Entropy Sum of Pairs Alignment Partial Order Alignment (POA) A-Bruijin (ABA) Approach to Multiple Alignment
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Multiple Alignment versus Pairwise Alignment Up until now we have only tried to align two sequences.
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Multiple Alignment versus Pairwise Alignment Up until now we have only tried to align two sequences. What about more than two? And what for?
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Multiple Alignment versus Pairwise Alignment Up until now we have only tried to align two sequences. What about more than two? And what for? A faint similarity between two sequences becomes significant if present in many Multiple alignments can reveal subtle similarities that pairwise alignments do not reveal
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Generalizing the Notion of Pairwise Alignment Alignment of 2 sequences is represented as a 2-row matrix In a similar way, we represent alignment of 3 sequences as a 3-row matrix   A T _ G C G _   A _ C G T _ A   A T C A C _ A Score: more conserved columns, better alignment
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Alignments = Paths in Align 3 sequences: ATGC, AATC,ATGC A A T -- C A -- T G C -- A T G C
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Alignment Paths 0 1 1 2 3 4 A A T -- C A -- T G C -- A T G C x coordinate
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Alignment Paths Align the following 3 sequences: ATGC, AATC,ATGC 0 1 1 2 3 4 0 1 2 3 3 4 A A T -- C A -- T G C -- A T G C x coordinate y coordinate
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Alignment Paths 0 1 1 2 3 4 0 1 2 3 3 4 A A T -- C A -- T G C 0 0 1 2 3 4 -- A T G C Resulting path in (x,y,z) space: (0,0,0) (1,1,0) (1,2,1) (2,3,2) (3,3,3) (4,4,4) x coordinate y coordinate z coordinate
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Aligning Three Sequences Same strategy as aligning two sequences Use a 3-D “Manhattan Cube”, with each axis representing a sequence to align For global alignments, go from source to sink source sink
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info 2-D vs 3-D Alignment Grid V W 2-D edit graph 3-D edit graph
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info 2-D cell versus 2-D Alignment Cell In 3-D , 7 edges in each unit cube In 2-D , 3 edges in each unit square
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Ch06_MultAlign - An Introduction to Bioinformatics...

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