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

Keith Robison robison at lipid.harvard.edu
Mon Jun 24 21:21:55 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
Department of Molecular & Cellular Biology
Department of Genetics 

robison at mito.harvard.edu 






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