java - How to build the scoring matrix for global sequence alignment? -
i have tried global sequence alignment between 2 strings. gives me wrong answer. way of generating scoring matrix below.
public void makescoringmatrix(string v,string w) { int ar[][]=new int[v.length()+1][w.length()+1]; for(int i=v.length()-1;i>=0;i--) { for(int j=w.length()-1;j>=0;j--) { if(v.charat(i)==w.charat(j)) ar[i][j]=ar[i+1][j+1]+1; else if(v.charat(i)!=w.charat(j)) ar[i][j]=ar[i+1][j+1]+0; else ar[i][j]=math.max(ar[i][j+1],math.max(ar[i+1][j],ar[i+1][j+1])); } } //printarray(ar); getglobalalignment(ar,v,w); } public void getglobalalignment(int ar[][],string v,string w) { int i=0,j=0,index=0; while(i<v.length() && j<w.length()) { if(v.charat(i)==w.charat(j)) { system.out.print(v.charat(i)); i++; j++; index++; } else if(ar[i+1][j]>ar[i][j+1]) { i++; } else { j++; } } } someone please me...!
try code...
public void makematrix(string v,string w) { int[][] maxdist=new int[v.length()+1][w.length()+1]; for(int i=0;i<=v.length();i++) { for(int j=0;j<=w.length();j++) { if(i==0) maxdist[i][j]=-j; else if(j==0) maxdist[i][j]=-i; else maxdist[i][j]=0; } } fillmatrix(maxdist, v, w); } public int weight(string v,string w,int i,int j) { if(v.charat(i-1)==w.charat(j-1)) return 1; else return -1; } public void fillmatrix(int[][] ar,string v,string w) { for(int i=1;i<=v.length();i++) { for(int j=1;j<=w.length();j++) { int scorediagonal=ar[i-1][j-1]+weight(v, w, i, j); int scoreleft=ar[i][j-1]-1; int scoreup=ar[i-1][j]-1; ar[i][j]=math.max(scorediagonal, math.max(scoreleft, scoreup)); } } } hope code looking for...
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