Global/Local/Multiple Alignments

by Boyang Wei

GlobalAlignment

How to run:  •  GlobalAlignment -s  seq1 seq2 (-m)

 •  GlobalAlignment -f   file1 file2 (-m)

 Sample output: rns202-15.cs.stolaf.edu% GlobalAlignment -s ABB ABABBAB -

ABBA - B   

GlobalAlignment

// represent each box in the matrixstruct box {  int row;                 // row index  int col;                 // column index  int score;               // best score  vector<box*> from;       // where does the score come from};

LocalAlignment

How to run:  •  LocalAlignment -s  seq1 seq2 (-m)

 •  LocalAlignment -f   file1 file2 (-m)

 Sample output: rns202-15.cs.stolaf.edu% LocalAlignment -f seq1.txt seq2.txtAC|TAC|T  G|TAC|

LocalAlignment

Sample output with matrix printed: rns202-15.cs.stolaf.edu% LocalAlignment -f seq1.txt seq2.txt -mAC|TAC|T  G|TAC|

      -    A    C    T    A    C    T    -     0    0    0    0    0    0    0    G   0    0    0    0    0    0    0    T    0    0    0    2    1    0    2    A    0    2    1    1    4    3    2    C    0    1    4    3    3    6    5    

Global & Local Alignment

Input:  • both programs require exact two sequences as input

 • not limited to A, T, G, C

 • don't require capitalized character

 • all kinds of characters will work

MultipleAlignment

How to run:  •  MultipleAlignment -s  seq1 seq2 seq3 ...

 •  MultipleAlignment -f   file

 Sample output: rns202-15.cs.stolaf.edu% MultipleAlignment -s ATGC ATG ATCATGCATG -AT - C 

MultipleAlignment

// class to store a character// its objects represent the letters in the sequence// NOTE! since the letter class is set up in this way, // it will store characters other than A, T, G, C as a gap,// so this program only works for input consisting of A, T, G, C

struct letter {  float A;     // percentage of A in this letter  float T;     // percentage of T in this letter  float G;     // percentage of G in this letter  float C;     // percentage of C in this letter  float gap;   // percentage of gap in this letter  ......}

MultipleAlignment

// a self-defined string class// to store the sequence/string as a sequence of letter objects

struct sequence {  vector<letter> seq;       // the sequence

  vector<int> gapPosition;  // the gap positions at the end of aligning

  int prev[2];              // index of the previous two sequences                                // (sometimes a sequence may be generated by                                //  combining two sequence)   ......}

MultipleAlignment

// calculate the score for two letter// either a match, mismatch, or partial match

float calculateScore(letter l1, letter l2) {  float matchPercent = min(l1.A, l2.A) +                                     min(l1.T, l2.T) +                                     min(l1.G, l2.G) +                                    min(l1.C, l2.C);  float misMatchPercent = 1 - matchPercent;  return matchPercent*matchScore +                         misMatchPercent*misMatchScore;}

MultipleAlignment

// combine two letters to generate a new oneletter sum(letter l1, letter l2) {  // if one of them is a gap, return the other one  if (l1.gap == 1)     return l2;  else if (l2.gap == 1)    return l1;  // otherwise, combine the percentages  else {    letter l((l1.A+l2.A)/2,               (l1.T+l2.T)/2,               (l1.G+l2.G)/2,               (l1.C+l2.C)/2,               (l1.gap+l2.gap)/2);   // could just put 0 for this line    return l;  }}

MultipleAlignment

Input:  • requires at least one sequence as input

 • if read from file:

o first line: the number of input sequenceso rest lines: one sequence per line