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
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?
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
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
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
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
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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