{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

Lec03-local

# Lec03-local - Local Alignment CMSC 423 Global Semi-global...

This preview shows pages 1–7. Sign up to view the full content.

Local Alignment CMSC 423

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

View Full Document
Global, Semi-global, Local Alignments Last time, we saw a dynamic programming algorithm for global alignment: both strings s and t must be completely matched: Semiglobal: Local: Gaps at starts and ends of some sequences come for free Best alignment between substrings of s and t. s t t s s t
Free gaps at ends of sequences best alignment between x and a prefx of y 0 1 2 3 4 5 8 9 10 11 12 9 8 7 6 5 4 3 2 1 0 9g 8g 7g 6g 5g 4g 3g 2g 1g 0 1g 2g 3g 4g 5g 6g 7g 8g 9g 10g 11g 12g OPT(n, m) best ignoring spaces matched to end of y x y C A G T T G C A A max of blue = A A G G T A T G A A T C best ignoring spaces matched to end of x max of orange =

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

View Full Document
Free gaps at the start of sequences 0 1 2 3 4 5 8 9 10 11 12 9 8 7 6 5 4 3 2 1 0 9g 8g 7g 6g 5g 4g 3g 2g 1g 0 0 0 0 0 0 0 0 0 0 0 0 0 ignore spaces matched to start of x x y C A G T T G C A A set blue = 0 to A A G G T A T G A A T C ignore spaces matched to start of y set orange = 0 to
Semiglobal Recap Can combine these: e.g. to allow free spaces matched to the start of x and both ends of y: set bottom row and left-most column to 0 and take the max of the rightmost column. Free spaces matched to What to do end of x take max of topmost row end of y take max of rightmost column start of x set bottommost row to 0 start of y set leftmost column to 0

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

View Full Document
Local Alignment s t Local alignment between s and t: Best alignment between a subsequence of s and a subsequence of t.
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

### Page1 / 17

Lec03-local - Local Alignment CMSC 423 Global Semi-global...

This preview shows document pages 1 - 7. Sign up to view the full document.

View Full Document
Ask a homework question - tutors are online