pairwiseAlignment in R

Question

[deepue]

I have been using the pairwiseAlignment function in the BioStrings package with the default parameters. I have noticed that there are possibilities of using different scoring matrices for the substitutionMatrix parameter. Could you please advise on how to identify the default scoring criteria used for the local alignment in this function ?

align <- pairwiseAlignment(seqA,seqB, type = "local")

Though few parameter values can be extracted through the writePairwiseAlignments function, I was not successful in getting the value for the substitutionMatrix.

writePairwiseAlignments(align)

Thanks.

Answer 1

[Jean-Karim Heriche]

As far as I can tell, there is no default substitution matrix, you have to provide one e.g.

subMat <- nucleotideSubstitutionMatrix(match = 3, mismatch = -1, baseOnly = TRUE, type = "DNA")

[deepue]

Thanks for your comment.

It is not a compulsory parameter. The function works even without a value for substitutionMatrix.

For example:

pairwiseAlignment(seqA,seqB, type = "local")

If we do not specify the value explicitly, what value it assumes ?