Short C implementation (around 500 lines of codes + comments) of the Gotoh algorithm, also known as the Needleman-Wunsch algorithm with affine gap penalties.

• C99-compliant, only uses stdio.h, stdlib.h, string.h, and ctype.h
• basic command-line interface
• read FASTA files
• read NCBI/EMBOSS scoring matrix files
• exact same results as EMBOSS Needle
• initial values in the dynamic programming arrays can be loaded from files

Due to the last point, the program can be used for experimenting with different scoring schemes, for example:

• gap opening penalties depending on the residues surrounding the gap
• substitution scores depending on the matched residues and their positions in the sequence
• doing something else than biological sequence alignment, such as dynamic time warping

Compile with this command:

gcc -std=c99 gotoh.c main.c -o align

Then type ./align and read the help message.

Basic example showing how to use the code:

gth_Seq sequenceX = gth_read_fasta("first_sequence.fasta");
gth_Seq sequenceY = gth_read_fasta("second_sequence.fasta");
gth_Sub matrix = gth_read_matrix("BLOSUM62");
int gapopen=10, gapextend=1, endopen=0, endextend=0;

gth_Arr array = gth_init(sequenceX.len, sequenceY.len);
gth_set_sub(array, sequenceX.res, sequenceY.res, matrix.score);
gth_set_gap(array, gapopen, gapextend, endopen, endextend);
int score = gth_align(array);

printf("Score: %d\n", score);
gth_putseq(stdout, sequenceX.res, array.gapX);
printf("\n");
gth_putseq(stdout, sequenceY.res, array.gapY);
printf("\n");

gth_free(array);
free(sequenceX.res);
free(sequenceY.res);

Durbin, Eddy, Krogh, Mitchison. Biological Sequence Analysis, Cambridge University Press, 1998.