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Thread: sequence alignment

  1. #1 sequence alignment 
    Forum Freshman
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    hi
    if i have this path between two sequences, I generated it randomly,
    how can alignment the two sequences according to this path?

    A C C T T T C

    A 1 1 0 0 0 0 0
    C 0 1 0 0 0 0 0
    G 0 0 1 0 0 0 0
    G 0 0 1 0 0 0 0
    C 0 0 0 1 0 0 0
    T 0 0 0 0 1 0 0
    T 0 0 0 0 0 1 0
    T 0 0 0 0 0 1 1
    C 0 0 0 0 0 0 1

    thanks in advance


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  3. #2  
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    Hi Huda,

    Interesting question but I'm not quite sure what you're trying to do.

    Is this for using bioinformatic program to align the sequnce ? or Trying to indentify part of the gene?


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  4. #3  
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    thanks,
    no,not necessary be biological sequences , consider it any sequence.
    in my application, I need to generate the path randomly, but I did not know how I can do the alignment the two sequences.
    please ,any suggestions may help.

    thanks again.
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  5. #4  
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    Quote Originally Posted by huda View Post
    thanks,
    no,not necessary be biological sequences , consider it any sequence.
    in my application, I need to generate the path randomly, but I did not know how I can do the alignment the two sequences.
    please ,any suggestions may help.

    thanks again.
    if u have any reference , any information about pairwise sequence alignment and PSO algorithm, i found some papers but about multiple not pairwise.
    i built algorithm depend on one paper.
    have queries and problems, please if u can help, let me know

    thanks in advance
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