Hi,
I have a small doubt regarding my program. Hope you will help me in solving that.

Example:

$a="agaaaagavvgglggy"
$b=<STDIN>;

let the input seq is "ttttttttttagaaaagavtttggyttttttt";

here the input matches with $a only with the letters in bold : ttttttttttagaaaagavtttggyttttttt

i want to know what we can do to give input showing both matches and mismatches in the input.(mismatch shold me shown as a hiphen)
That means the output should be like this:
The given sequence matches with the pattern at - - - - - - - - - - agaaaagav- - -ggy - - - - - - -

Hope you will help me in solving out this.

Thanks in advance,
siri

Jus try out this . I am trying "aga" as the string to match.

#!/usr/bin/perl -w
$a="aga";
print "input string : \n";
$b=<STDIN>;
if ( $b=~/($a)/ )
{
print "matched part: $1 \n";
print " part before matched $` \n";
print " part after matched $' ";
}