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

Question

[hmedinasantacruz]

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.

[Fatima]

If you click on "More options" You can see which scoring matrices you can choose from. The default is "BLOSUM62"

https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt

https://bio.libretexts.org/Bookshelves/Cell_and_Molecular_Biology/Book%3A_Investigations_in_Molecular_Cell_Biology_(O'Connor)/09%3A_Protein_Conservation/9.05%3A_BLOSUM62_scoring_matrix_for_amino_acid_substitutions

Answer 1

[hmedinasantacruz]

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.

[Fatima]

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.