{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

multiple_alignment

# multiple_alignment - University of North Texas Biocomputing...

This preview shows pages 1–12. Sign up to view the full content.

Biocomputing University of North Texas Multiple Alignment Source: www.bioalgorithms.info

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
University of North Texas Biocomputing Multiple Alignment versus Pairwise Alignment Up until now we have only tried to align two sequences.
University of North Texas Biocomputing 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

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
University of North Texas Biocomputing 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
University of North Texas Biocomputing Alignments = Paths in Align 3 sequences: ATGC, AATC,ATGC A A T -- C A -- T G C -- A T G C

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
University of North Texas Biocomputing 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
University of North Texas Biocomputing 2-D vs 3-D Alignment Grid V W 2-D edit graph 3-D edit graph

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
University of North Texas Biocomputing Architecture of 3-D Alignment Cell (i-1,j-1,k-1) (i,j-1,k-1) (i,j-1,k) (i-1,j-1,k) (i-1,j,k) (i,j,k) (i-1,j,k-1) (i,j,k-1)
University of North Texas Biocomputing Multiple Alignment: Dynamic Programming s i,j,k = max 2200 δ ( x, y, z ) is an entry in the 3-D scoring matrix s i-1,j-1,k-1 + (v i , w j , u k ) s i-1,j-1,k + (v i , w j , _ ) s i-1,j,k-1 + (v i , _, u k ) s i,j-1,k-1 + (_, w j , u k ) s i-1,j,k + (v i , _ , _) s i,j-1,k + (_, w j , _) s i,j,k-1 + (_, _, u k ) cube diagonal: no indels face diagonal: one indel edge diagonal: two indels

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
University of North Texas Biocomputing Multiple Alignment: Running Time For 3 sequences of length n , the run time is 7 n 3 ; O( n 3 ) For k sequences, build a k -dimensional Manhattan, with run time ( 2 k -1)( n k ); O( 2 k n k ) Conclusion: dynamic programming approach for alignment between two sequences is easily extended to k sequences but it is impractical due to exponential running time
University of North Texas Biocomputing Multiple Alignment Induces Pairwise Alignments

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

### Page1 / 36

multiple_alignment - University of North Texas Biocomputing...

This preview shows document pages 1 - 12. Sign up to view the full document.

View Full Document
Ask a homework question - tutors are online