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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