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
Department of Molecular & Cellular Biology
Department of Genetics
robison at mito.harvard.edu
