Question: calculating alignment score with EMBOSS needle
0
gravatar for Fadel
2.9 years ago by
Fadel10
Malaysia
Fadel10 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 :))

screenshot

emboss alignment • 1.5k views
ADD COMMENTlink modified 2.9 years ago by Asaf5.6k • written 2.9 years ago by Fadel10
2
gravatar for Asaf
2.9 years ago by
Asaf5.6k
Israel
Asaf5.6k wrote:

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

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Asaf5.6k

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 ?

ADD REPLYlink written 2.9 years ago by Fadel10
1

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

ADD REPLYlink written 2.9 years ago by Asaf5.6k

its much more clean now, thanks again Asaf.

ADD REPLYlink written 2.9 years ago by Fadel10
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