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calculating alignment score with EMBOSS needle

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 :))

screenshot

alignment emboss
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updated by Asaf Asaf • written by Fadel • Fadel

1 answer

End gaps are not scored so you have 8*(-10) + 8*(-1) = -88 instead of -114 which brings you exactly to 52.

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written by Asaf Asaf

thanks Asaf, so I can say that the best score is not calculated from the scoring matrix directly by taking the value of the most right, most low cell ?

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written by Fadel • Fadel

It's taken from the maximal value in the most right column or the lowest row.

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written by Asaf Asaf

its much more clean now, thanks again Asaf.

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written by Fadel • Fadel

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