Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Incorrect alignment/score when using gap penalty = Inf #4

Open
traversc opened this issue Oct 26, 2020 · 0 comments
Open

Incorrect alignment/score when using gap penalty = Inf #4

traversc opened this issue Oct 26, 2020 · 0 comments

Comments

@traversc
Copy link

I want to do an alignment where pattern is contained within subject without gaps. Here's a quick example:

 q <- "TCAGT"
s <- "TCAGGTCAGT"
smat <- nucleotideSubstitutionMatrix(match = 0, mismatch = -1, baseOnly = TRUE)

pairwiseAlignment(q, s, substitutionMatrix=smat, gapOpening=Inf, gapExtension=Inf, type = "global-local")
Global-Local PairwiseAlignmentsSingleSubject (1 of 1)
pattern:     TCAGT
subject: [1] TCAGG
score: -1 

pairwiseAlignment(q, s, substitutionMatrix=smat, gapOpening=100, gapExtension=100, type = "global-local")
Global-Local PairwiseAlignmentsSingleSubject (1 of 1)
pattern:     TCAGT
subject: [6] TCAGT
score: 0 
@hpages hpages transferred this issue from Bioconductor/Biostrings Mar 23, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant