When we give an input sequence , the tool should match with the pattern and give the matches and mismatches in the output.
i will give you 2 small examples. if you cant get it pls let me know.
i will try to give a clear idea.
$a=APPLE; # let it be a pattern
$b=<STDIN>; # input sequence
suppose my input sequence ($b) is : MYAPPLES
Then the input ($b) will match with $a only from 3rd letter to 7th letter.( i.e APPLE)
i want to get out put as below:
The matching region is - - APPLE- (i.e mismatches should be shown as hiphen)
If the pattern is "MYAPPLE" and the input is "APPLEMY"
Then the output should be:
- -APPLE- -
i.e the first 2 hiphens represent gaps and last 2 hiphens represent mismatches.
$a="agaaaagavvgglggy" # a pattern signature
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.(mismatches in the seq should be shown as a hiphen)
That means the output should be like this:
The given sequence matches with the pattern at - - - - - - - - - - agaaaagav- - -ggy - - - - - -