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:-
score = BestFit(char* seq1, char* seq2, char* seq3, char* seq4,
int parm1, int parm2,,,)
where seq1 & seq2 are the starting ASCII string of sequences
seq3,& seq4 are the best aligned matches of these two sequences
parm1, parm2 etc are starting parameters for scoreing etc.
