MSA code 1
Due to my lack of coding ability, I couldn't solve some errors.
#!/usr/bin/perl
use 5.010;
use strict;
use warnings;
my $seq1= 'AAGAATAGTATTTCGCTTTTTTATA';
my $seq2= 'AGAAATAGTATTTCGGTTAATTATA';
my $seq3= 'AGACATACTAATTCGGTCCATTATA';
my @matrix;
$matrix[0][0]{score} = 0;
$matrix[0][0]{pointer} = "none";
for(my $j = 1; $j <= length($seq1); $j++) {
$matrix[0][$j]{score} = $GAP * $j;
$matrix[0][$j]{pointer} = "left";
}
for (my $i = 1; $i <= length($seq2); $i++) {
$matrix[$i][0]{score} = $GAP * $i;
$matrix[$i][0]{pointer} = "up";
}
# fill
for(my $i = 1; $i <= length($seq2); $i++) {
for(my $j = 1; $j <= length($seq1); $j++) {
my ($diagonal_score, $left_score, $up_score);
# calculate match score
my $letter1 = substr($seq1, $j-1, 1);
my $letter2 = substr($seq2, $i-1, 1);
+
if ($letter1 eq $letter2) {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MATCH;
}
else {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MISMATCH;
}
# calculate gap scores
$up_score = $matrix[$i-1][$j]{score} + $GAP;
$left_score = $matrix[$i][$j-1]{score} + $GAP;
# choose best score
if ($diagonal_score >= $up_score) {
if ($diagonal_score >= $left_score) {
$matrix[$i][$j]{score} = $diagonal_score;
$matrix[$i][$j]{pointer} = "diagonal";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
} else {
if ($up_score >= $left_score) {
$matrix[$i][$j]{score} = $up_score;
$matrix[$i][$j]{pointer} = "up";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
}
}
}
# trace-back
my $align1 = "";
my $align2 = "";
# start at last cell of matrix
my $j = length($seq1);
my $i = length($seq2);
while (1) {
last if $matrix[$i][$j]{pointer} eq "none"; # ends at first cell o
+f matrix
if ($matrix[$i][$j]{pointer} eq "diagonal") {
$align1 .= substr($seq1, $j-1, 1);
$align2 .= substr($seq2, $i-1, 1);
$i--;
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "left") {
$align1 .= substr($seq1, $j-1, 1);
$align2 .= "-";
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "up") {
$align1 .= "-";
$align2 .= substr($seq2, $i-1, 1);
$i--;
}
}
$align1 = reverse $align1;
$align2 = reverse $align2;
print "$align1\n";
print "$align2\n";
$matrix[0][0]{score} = 0;
$matrix[0][0]{pointer} = "none";
for(my $j = 1; $j <= length($seq1); $j++) {
$matrix[0][$j]{score} = $GAP * $j;
$matrix[0][$j]{pointer} = "left";
}
for (my $i = 1; $i <= length($seq3); $i++) {
$matrix[$i][0]{score} = $GAP * $i;
$matrix[$i][0]{pointer} = "up";
}
# fill
for(my $i = 1; $i <= length($seq3); $i++) {
for(my $j = 1; $j <= length($seq1); $j++) {
my ($diagonal_score, $left_score, $up_score);
# calculate match score
my $letter1 = substr($align1, $j-1, 1);
my $letter3 = substr($seq3, $i-1, 1);
+
if ($letter1 eq $letter3) {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MATCH;
}
else {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MISMATCH;
}
# calculate gap scores
$up_score = $matrix[$i-1][$j]{score} + $GAP;
$left_score = $matrix[$i][$j-1]{score} + $GAP;
# choose best score
if ($diagonal_score >= $up_score) {
if ($diagonal_score >= $left_score) {
$matrix[$i][$j]{score} = $diagonal_score;
$matrix[$i][$j]{pointer} = "diagonal";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
} else {
if ($up_score >= $left_score) {
$matrix[$i][$j]{score} = $up_score;
$matrix[$i][$j]{pointer} = "up";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
}
}
}
# trace-back
my $alignalign1 = "";
my $align3 = "";
# start at last cell of matrix
my $j = length($seq1);
my $i = length($seq3);
while (1) {
last if $matrix[$i][$j]{pointer} eq "none"; # ends at first cell o
+f matrix
if ($matrix[$i][$j]{pointer} eq "diagonal") {
$alignalign1 .= substr($align1, $j-1, 1);
$align3 .= substr($seq3, $i-1, 1);
$i--;
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "left") {
$alignalign1 .= substr($align1, $j-1, 1);
$align3 .= "-";
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "up") {
$alignalign1 .= "-";
$align3 .= substr($seq3, $i-1, 1);
$i--;
}
}
$alignalign1 = reverse $alignalign1;
$align3 = reverse $align3;
print "$alignalign1\n";
print "$align3\n";
$matrix[0][0]{score} = 0;
$matrix[0][0]{pointer} = "none";
for(my $j = 1; $j <= length($seq1); $j++) {
$matrix[0][$j]{score} = $GAP * $j;
$matrix[0][$j]{pointer} = "left";
}
for (my $i = 1; $i <= length($seq3); $i++) {
$matrix[$i][0]{score} = $GAP * $i;
$matrix[$i][0]{pointer} = "up";
}
# fill
for(my $i = 1; $i <= length($seq3); $i++) {
for(my $j = 1; $j <= length($seq2); $j++) {
my ($diagonal_score, $left_score, $up_score);
# calculate match score
my $letter2 = substr($align2, $j-1, 1);
my $letter3 = substr($seq3, $i-1, 1);
+
if ($letter2 eq $letter3) {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MATCH;
}
else {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MISMATCH;
}
# calculate gap scores
$up_score = $matrix[$i-1][$j]{score} + $GAP;
$left_score = $matrix[$i][$j-1]{score} + $GAP;
# choose best score
if ($diagonal_score >= $up_score) {
if ($diagonal_score >= $left_score) {
$matrix[$i][$j]{score} = $diagonal_score;
$matrix[$i][$j]{pointer} = "diagonal";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
} else {
if ($up_score >= $left_score) {
$matrix[$i][$j]{score} = $up_score;
$matrix[$i][$j]{pointer} = "up";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
}
}
}
# trace-back
my $alignalign2 = "";
my $align3 = "";
# start at last cell of matrix
my $j = length($seq2);
my $i = length($seq3);
while (1) {
last if $matrix[$i][$j]{pointer} eq "none"; # ends at first cell o
+f matrix
if ($matrix[$i][$j]{pointer} eq "diagonal") {
$alignalign2 .= substr($align2, $j-1, 1);
$align3 .= substr($seq3, $i-1, 1);
$i--;
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "left") {
$alignalign2 .= substr($align2, $j-1, 1);
$align3 .= "-";
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "up") {
$alignalign2 .= "-";
$align3 .= substr($seq3, $i-1, 1);
$i--;
}
}
$alignalign2 = reverse $alignalign2;
$align3 = reverse $align3;
print "$alignalign1\n";
print "$alignalign2\n";
print "$align3\n";
