Dear Edward,

This was my approach to your problem. It runs through all the sequences you give it in the @sequences array looking for the one with the biggest gaps, and kicking out any where the letter order isn't right. It populates the @in_the_running array with sequences that will work. While this is happening, it makes sure that the sequence with the biggest gap stays at the front of the array (index 0). It then prints the sequence with the biggest gap, and runs through the rest of the sequences that qualified - each sequence it compares against the one with the biggest gap, letter by letter. If it matches, it prints a letter - if it doesn't it prints a dash.

This is one of those fun problems where multiple approaches could be applied - I hope mine assists you with yours!

Best,
  -Adam
@in = split(//,<STDIN>); pop(@in);

$regex = '.*'.join('(.*)',@in).'.*';

@sequences = qw/ABCDHA ACDBGJ CADHMK ABICID/;

for (@sequences) {
  @letters = split(//,$_);
  s/.*($in[0].*$in[$#in]).*/$1/;
  if ((@gaps) = (m/$regex/o)){
    if (length(join('',@gaps)) > $biglen) { unshift(@in_the_running, $
+_); $biglen = length(join('',@gaps)) }
    else { push(@in_the_running, $_) }
  }
}

print $in_the_running[0], "\n";

@base = split(//,$in_the_running[0]);
for my $seqno (1..$#in_the_running) {
  @seq = split(//,$in_the_running[$seqno]);
  for $q (@base) {
    if ($seq[0] eq $q) { print $q; shift(@seq); next }
    else { print '-' }
  }
  print "\n";
}

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In reply to Re: Simple String Alignment by Adrade
in thread Simple String Alignment by monkfan

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