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What is the Score Matrix in the web server EMBOSS Needle for pairwise alingment?

This post is to see what is the scoring matrix of the Nedleman and Wunsch algorithm implemented at https://www.ebi.ac.uk/Tools/psa/emboss_needle/? My query is because this generates very different results than other applications where only Match and missmatch scores are entered. Also, I need the scoring matrix to be able to check the hardware implementation compared to the one on the page.

dinamic programing dna score matrix nedlemanwunsch
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written by hmedinasantacruz • hmedinasantacruz

1 answer

my question was regarding the alignment of DNA not protein, however I have already written to the designers of the software and they have answered me. apparently the alignment uses a matrix of Match = 1, missmatch = 0 and Gaps what the user enters. thanks for your help.

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written by hmedinasantacruz • hmedinasantacruz

For DNA sequences, as default EMBOSS Needle uses ENDfull (DNAfull)

http://rosalind.info/glossary/dnafull/

A   T   G   C   
A   5  -4  -4  
T  -4   5  -4  
G  -4  -4   5  
C  -4  -4  -4

Which can be simplified into match=1 and mistmatch=0.

A scoring matrix is read that contains values for every possible residue or nucleotide match.

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written by Fatima Fatima

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