Scribd Logo
Upload

Welcome to Scribd!

  • Skoringmatriks

    Uploaded by

    diyah
    4 views1 page
    The document describes troubleshooting errors when trying to perform a global pairwise sequence alignment in R using the Biostrings package. It shows correcting typos like changing "baseonly" to "baseOnly", removing unused arguments, and fixing the spelling of "gapExtension". The alignment is successfully run after resolving these issues.

    Original Description:

    Original Title

    skoringmatriks.docx

    Copyright

    © © All Rights Reserved

    Available Formats

    DOCX, PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    Report this Document
    The document describes troubleshooting errors when trying to perform a global pairwise sequence alignment in R using the Biostrings package. It shows correcting typos like changing "baseonly" to "baseOnly", removing unused arguments, and fixing the spelling of "gapExtension". The alignment is successfully run after resolving these issues.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    4 views1 page

    Skoringmatriks

    Uploaded by

    diyah
    The document describes troubleshooting errors when trying to perform a global pairwise sequence alignment in R using the Biostrings package. It shows correcting typos like changing "baseonly" to "baseOnly", removing unused arguments, and fixing the spelling of "gapExtension". The alignment is successfully run after resolving these issues.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    of 1

    library(Biostrings)

    > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseonly=TRUE)


    Error in nucleotideSubstitutionMatrix(match = 2, mismatch = -1, baseonly = TRUE) :
    unused argument (baseonly = TRUE)
    > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseonly=TRUE)
    Error in nucleotideSubstitutionMatrix(match = 2, mismatch = -1, baseonly = TRUE) :
    unused argument (baseonly = TRUE)
    > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseOnly = =TRUE)
    Error: unexpected '=' in "skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1,
    baseOnly = ="
    > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseOnly =TRUE)
    > skoringmatriks
    A C G T
    A 2 -1 -1 -1
    C -1 2 -1 -1
    G -1 -1 2 -1
    T -1 -1 -1 2
    > sekuens1<-"ACGTGACTCCTA"
    > sekuens2<-"GTCAGTAATCG"
    > penyejajaranglobal<pairwiseAligment(sekuens1,sekuens2,substitutionMatrix=skoringmatriks,gapopening=2,gapExtention=-8,scoreonly=FALSE)
    Error: could not find function "pairwiseAligment"
    > penyejajaranglobal<pairwiseAlignment(sekuens1,sekuens2,substitutionMatrix=skoringmatriks,gapopening=2,gapExtention=-8,scoreonly=FALSE)
    Error in .local(pattern, subject, ...) :
    unused arguments (gapopening = -2, gapExtention = -8, scoreonly = FALSE)
    > penyejajaranglobal<pairwiseAlignment(sekuens1,sekuens2,substitutionMatrix=skoringmatriks,gapOpening=2,gapExtention=-8,scoreOnly=FALSE)
    Error in .local(pattern, subject, ...) :
    unused argument (gapExtention = -8)
    > penyejajaranglobal<pairwiseAlignment(sekuens1,sekuens2,substitutionMatrix=skoringmatriks,gapOpening=2,gapExtension=-8,scoreOnly=FALSE)
    > penyejajaranglobal
    Global PairwiseAlignmentsSingleSubject (1 of 1)
    pattern: [1] ACGTGACTCCT
    subject: [1] GTCAGTAATCG
    score: -15

    >

    You might also like