**10**wrote:

Im trying to implement Needleman-Wunch algorithm with affine gap penalties, and to do so I compare my results with EMBOSS needle output. Yet I have a problem with calculating the best score.

using DNAFULL matrix and gapopen = 10, gap extend= 1

Seq1: TGCTAGTATAAACCTTATGGTATCTGCAGCAGAGGTTTCTTTAATCTCTCAATAGTAGATGCTTTGAAAC Seq2: TTATCTATAATTTGGTATTGTAATGACAGTTTGTGTTTGGTTTTTTCTTCAGTAT

and the result score is 52, while we have

matches 36 * 5 = 180

mismatches 10 *(-4) = -40

gap-o 9 *(-10) = -90

gap-e 24 *(-1) = -24

the score should be 26 but I got 52 which I couldn't understand why! I appreciate any explanation :))