This preview has intentionally blurred sections. Sign up to view the full version.
View Full Document
Unformatted text preview: 1. [Answer] (1) Algorithm unrestricted on k . Algorithm 1 Pattern Matching without length requirment t ( i, 0) ⇐ 0, for all i t (0 , j ) ⇐ t (0 , j − 1) + σ (“ ” , t [ j ]), for all j for i = 1 to m do for j = 1 to n do t ( i, j ) = max t ( i − 1 , j ) + σ (“ ” , T [ i ]) t ( i, j − 1) + σ (“ ” , P [ j ]) t ( i − 1 , j − 1) + σ ( T [ i ] , p [ j ]) end for end for return argmax j t [ j, m ] (2) Algorhithm with length requirement on k . Define t [ i, l, j ] to be the maximum score of the global alignment between P [1 , j ] and T [ i, i + l ]. Let  P  = m and  T  = n . See the algorithm in the next page. Algorithm 2 Pattern Matching with length requirment for i = 1 to m do t [ i, , 0] = 0 for l = 1 to m do t [ i, l, 0] = t [ i, l − 1 , 0] + σ ( T [ i ] , “ ”) end for for j = 1 to m do t [ i, , j ] = t [ i, , j − 1] + σ (“ ” , P [ j ]) end for end for for i = 1 to m do for j = 1 to n do for l = 1 to n − i do t [ i, l, j ] = max t [ i, l − 1 , j − 1] + σ ( T [ i + 1] , P [ j ]) t [ i, l − 1 , j ] + σ ( T [ i + 1] , “ ”) t ( i, l, j − 1] + σ (“ ” , P [ j ]) end for end for end for return max i,l ≥ k t [ i, l, m ] 2. [Answer] The tablecomputing step and the traceback step need not change....
View
Full
Document
This note was uploaded on 10/01/2009 for the course CS BCB/Co taught by Professor Olivereulenstein during the Fall '06 term at Iowa State.
 Fall '06
 OLIVEREULENSTEIN

Click to edit the document details