如何修改Smith和Waterman perl脚本以加快速度？

Question

我找到了这个perl脚本,但我有太多的序列需要分析.我想知道是否可以对其进行优化？我在它上面推出了NYTProf,看到部分"计算匹配分数","计算差距分数"和"选择最佳分数"需要花费大量时间.我是否必须修改数据结构？谢谢您的帮助.

perl脚本的参考:

    # Smith-Waterman  Algorithm
# from this website http://etutorials.org/Misc/blast/Part+II+Theory/Chapter+3.+Sequence+Alignment/3.2+Local+Alignment+Smith-Waterman/

# Smith-Waterman  Algorithm

# usage statement
die "usage: $0 <sequence 1> <sequence 2>\n" unless @ARGV == 2;

# get sequences from command line
my ($seq1, $seq2) = @ARGV;

# scoring scheme
my $MATCH    =  1; # +1 for letters that match
my $MISMATCH = -1; # -1 for letters that mismatch
my $GAP      = -1; # -1 for any gap

# initialization
my @matrix;
$matrix[0][0]{score}   = 0;
$matrix[0][0]{pointer} = "none";
for(my $j = 1; $j <= length($seq1); $j++) {
    $matrix[0][$j]{score}   = 0;
    $matrix[0][$j]{pointer} = "none";
}
for (my $i = 1; $i <= length($seq2); $i++) {
    $matrix[$i][0]{score}   = 0;
    $matrix[$i][0]{pointer} = "none";
}

# fill
my $max_i     = 0;
my $max_j     = 0;
my $max_score = 0;

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;

        if ($diagonal_score <= 0 and $up_score <= 0 and $left_score <= 0) {
            $matrix[$i][$j]{score}   = 0;
            $matrix[$i][$j]{pointer} = "none";
            next; # terminate this iteration of the loop
        }

        # 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";
            }
        }

        # set maximum score
        if ($matrix[$i][$j]{score} > $max_score) {
            $max_i     = $i;
            $max_j     = $j;
            $max_score = $matrix[$i][$j]{score};
        }
    }
}

# trace-back

my $align1 = "";
my $align2 = "";

my $j = $max_j;
my $i = $max_i;

while (1) {
    last if $matrix[$i][$j]{pointer} eq "none";

    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";

Answer 1

你可以试着避免一遍又一遍地做同样的事情.

1. 您可以尝试在循环之前将字符中的序列拆分一次,而不是通过索引使用最可能更快的访问,而不是从序列中删除单个字符.

   例:

   my $string = "Hello, how are you?";
   my @chars = split //, $string;  # Or: unpack 'a*', $string
   print "Eighth char: $chars[7]\n";
   

2. my $letter2 = substr($seq2, $i-1, 1);可以转到外部循环,因为j内循环永远不会改变.

   for(my $i = 1; $i <= length($seq2); $i++) {
       my $letter2 = substr($seq2, $i-1, 1);
       for(my $j = 1; $j <= length($seq1); $j++) {
   

3. 避免使用速度较慢且复杂的C风格循环.

   for my $i (1..length($seq2)) {
       my $letter2 = substr($seq2, $i-1, 1);
       for my $j (1..length($seq1)) {
   

4. 而不是字符串,使用整数的值pointer.您可以使用常量来保持其可读性.

   use constant {
      POINTER_NONE => 0,
      POINTER_LEFT => 1,
      ...
   };
   

5. 预先计算$j-1也$i-1可能带来一个小优势.

请注意,您应该在每次更改之前和之后分析代码,以查看速度是否会增加.

所有这些都是微小的改进.真正的问题是你有一个二次算法.