Package: pwalign 1.1.0

Hervé Pagès

pwalign: Perform pairwise sequence alignments

The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Authors:Patrick Aboyoun [aut], Robert Gentleman [aut], Hervé Pagès [cre]

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pwalign.pdf |pwalign.html✨
pwalign/json (API)
NEWS

# Install 'pwalign' in R:
install.packages('pwalign', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/pwalign/issues

Datasets:
  • BLOSUM100 - Predefined scoring matrices
  • BLOSUM45 - Predefined scoring matrices
  • BLOSUM50 - Predefined scoring matrices
  • BLOSUM62 - Predefined scoring matrices
  • BLOSUM80 - Predefined scoring matrices
  • PAM120 - Predefined scoring matrices
  • PAM250 - Predefined scoring matrices
  • PAM30 - Predefined scoring matrices
  • PAM40 - Predefined scoring matrices
  • PAM70 - Predefined scoring matrices
  • phiX174Phage - Versions of bacteriophage phiX174 complete genome and sample short reads
  • quPhiX174 - Versions of bacteriophage phiX174 complete genome and sample short reads
  • srPhiX174 - Versions of bacteriophage phiX174 complete genome and sample short reads
  • wtPhiX174 - Versions of bacteriophage phiX174 complete genome and sample short reads

On BioConductor:pwalign-1.1.0(bioc 3.20)pwalign-1.0.0(bioc 3.19)

bioconductor-package

41 exports 6.26 score 18 dependencies 104 dependents

Last updated 2 months agofrom:402ad83031

Exports:alignedalignedPatternalignedSubjectas.matrixcompareStringsconsensusMatrixcoveragedeletionenderrorSubstitutionMatricesindelinsertionmismatchmismatchSummarymismatchTablencharneditnindelnmatchnmismatchnucleotideSubstitutionMatrixpairwiseAlignmentPairwiseAlignmentsPairwiseAlignmentsSingleSubjectparallel_slot_namesparallelVectorNamespatternpidqualitySubstitutionMatricesscoreshowstartstringDistsubjectsummarytoStringtypeunalignedViewswidthwritePairwiseAlignments

Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc

Pairwise Sequence Alignments

Rendered fromPairwiseAlignments.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2024-03-21
Started: 2024-03-21

Readme and manuals

Help Manual

Help pageTopics
Utility functions related to sequence alignmentalign-utils compareStrings compareStrings,AlignedXStringSet0,AlignedXStringSet0-method compareStrings,character,character-method compareStrings,PairwiseAlignments,missing-method compareStrings,XString,XString-method compareStrings,XStringSet,XStringSet-method consensusMatrix,PairwiseAlignmentsSingleSubject-method coverage,AlignedXStringSet0-method coverage,PairwiseAlignmentsSingleSubject-method coverage,PairwiseAlignmentsSingleSubjectSummary-method mismatch,AlignedXStringSet0,missing-method mismatchSummary mismatchSummary,AlignedXStringSet0-method mismatchSummary,PairwiseAlignmentsSingleSubject-method mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method mismatchSummary,QualityAlignedXStringSet-method mismatchTable mismatchTable,AlignedXStringSet0-method mismatchTable,PairwiseAlignments-method mismatchTable,QualityAlignedXStringSet-method nedit nedit,PairwiseAlignments-method nedit,PairwiseAlignmentsSingleSubjectSummary-method nmatch,PairwiseAlignments,missing-method nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method nmismatch,AlignedXStringSet0,missing-method nmismatch,PairwiseAlignments,missing-method nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method
AlignedXStringSet and QualityAlignedXStringSet objectsaligned aligned,AlignedXStringSet0-method AlignedXStringSet AlignedXStringSet-class AlignedXStringSet0 AlignedXStringSet0-class as.character,AlignedXStringSet0-method class:AlignedXStringSet class:AlignedXStringSet0 class:QualityAlignedXStringSet end,AlignedXStringSet0-method indel indel,AlignedXStringSet0-method nchar,AlignedXStringSet0-method nindel nindel,AlignedXStringSet0-method parallelVectorNames,AlignedXStringSet0-method parallel_slot_names,AlignedXStringSet0-method QualityAlignedXStringSet QualityAlignedXStringSet-class ranges,AlignedXStringSet0-method seqtype,AlignedXStringSet0-method show,AlignedXStringSet0-method start,AlignedXStringSet0-method toString,AlignedXStringSet0-method unaligned unaligned,AlignedXStringSet0-method width,AlignedXStringSet0-method
InDel objectsclass:InDel deletion deletion,InDel-method InDel InDel-class insertion insertion,InDel-method
Optimal Pairwise AlignmentpairwiseAlignment pairwiseAlignment,ANY,ANY-method pairwiseAlignment,ANY,QualityScaledXStringSet-method pairwiseAlignment,QualityScaledXStringSet,ANY-method pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objectsaligned,PairwiseAlignmentsSingleSubject-method alignedPattern alignedPattern,PairwiseAlignments-method alignedSubject alignedSubject,PairwiseAlignments-method as.character,PairwiseAlignmentsSingleSubject-method as.matrix,PairwiseAlignmentsSingleSubject-method class:PairwiseAlignments class:PairwiseAlignmentsSingleSubject class:PairwiseAlignmentsSingleSubjectSummary deletion,PairwiseAlignments-method indel,PairwiseAlignments-method insertion,PairwiseAlignments-method length,PairwiseAlignmentsSingleSubjectSummary-method nchar,PairwiseAlignments-method nchar,PairwiseAlignmentsSingleSubjectSummary-method nindel,PairwiseAlignments-method nindel,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments PairwiseAlignments,character,character-method PairwiseAlignments,character,missing-method PairwiseAlignments,XString,XString-method PairwiseAlignments,XStringSet,missing-method PairwiseAlignments-class PairwiseAlignmentsSingleSubject PairwiseAlignmentsSingleSubject,character,character-method PairwiseAlignmentsSingleSubject,character,missing-method PairwiseAlignmentsSingleSubject,XString,XString-method PairwiseAlignmentsSingleSubject,XStringSet,missing-method PairwiseAlignmentsSingleSubject-class PairwiseAlignmentsSingleSubjectSummary PairwiseAlignmentsSingleSubjectSummary-class parallel_slot_names,PairwiseAlignments-method pattern,PairwiseAlignments-method score,PairwiseAlignments-method score,PairwiseAlignmentsSingleSubjectSummary-method seqtype,PairwiseAlignments-method show,PairwiseAlignments-method show,PairwiseAlignmentsSingleSubjectSummary-method subject,PairwiseAlignments-method summary,PairwiseAlignmentsSingleSubject-method toString,PairwiseAlignmentsSingleSubject-method type type,PairwiseAlignments-method type,PairwiseAlignmentsSingleSubjectSummary-method Views,PairwiseAlignmentsSingleSubject-method
Write a PairwiseAlignments object to a filePairwiseAlignments-io writePairwiseAlignments
Versions of bacteriophage phiX174 complete genome and sample short readsphiX174Phage quPhiX174 srPhiX174 wtPhiX174
Percent Sequence Identitypid pid,PairwiseAlignments-method
Predefined scoring matricesBLOSUM100 BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 PAM30 PAM40 PAM70 predefined_scoring_matrices
String Distance/Alignment Score MatrixstringDist stringDist,character-method stringDist,QualityScaledXStringSet-method stringDist,XStringSet-method
Utilities to generate substitution matriceserrorSubstitutionMatrices nucleotideSubstitutionMatrix qualitySubstitutionMatrices substitution_matrices