A self contained C++ (or c) sequence alignement function

John Powell jip at helix.nih.gov
Tue Jun 25 13:54:43 EST 1996


John Monahan (monahan at ix.netcom.com) wrote:

:: Does anybody out there have code for a self contained nucleotide
:: sequence alignement function that once called returns the best fit
:: alignement of two sequences.  I have been looking through the code for
:: FASTA and BLAST based programs and am frustated to find that the real
:: kernal of the code is buried deep with all kinds of hooks to other
:: places in the code. Has any body got/tried to write a function along
:: the lines:-

:You might look into SIM, written by Xiaoqu Huang (sp?).  It is a Smith-Waterman
:implementation, and as I remember it the main function comes pretty close
:to what you want.

:Good luck!

;Keith Robison
:Harvard University


sim was indeed by Xiaoqiu Huang...

 Please cite the paper
    "A Time-Efficient, Linear-Space Local Similarity Algorithm"
        (Advances in Applied Mathematics, 12: 337-357, 1991)

              Xiaoqiu Huang
              Department of Computer Science
              Michigan Technological University
              Houghton, MI 49931

              Webb Miller
              Department of Computer Science
              The Pennsylvania State University
              University Park, PA 16802

But I beleive it only aligns two sequences (or one against itself).

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