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  1. #1
    Join Date
    Jan 2008

    Exclamation Unanswered: Matches and mismatches in perl

    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.

    example 1:

    $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 - - - - - -

  2. #2
    Join Date
    Oct 2002
    Baghdad, Iraq
    You're probably looking for a diff algorithm.

    Beyond that, you haven't specified the problem completely enough to come up with an actual answer. And it sounds like a homework problem to me.

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