Introduction | Pairwise Sequence Alignment Problems | Main Pairwise Sequence Alignment Function | Pairwise Sequence Alignment Classes | Pairwise Sequence Alignment Helper Functions | Edit Distances | Application: Using Evolutionary Models in Protein Alignments | Application: Removing Adapters from Sequence Reads | Application: Quality Assurance in Sequencing Experiments | Computation Profiling | Computing alignment consensus matrices | Exercise Answers | Session Information
Package: pwalign 1.9.1
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:
pwalign_1.9.1.tar.gz
pwalign_1.9.1.zip(r-4.7)pwalign_1.9.1.zip(r-4.6)pwalign_1.9.1.zip(r-4.5)
pwalign_1.9.1.tgz(r-4.6-x86_64)pwalign_1.9.1.tgz(r-4.6-arm64)pwalign_1.9.1.tgz(r-4.5-x86_64)pwalign_1.9.1.tgz(r-4.5-arm64)
pwalign_1.9.1.tar.gz(r-4.7-arm64)pwalign_1.9.1.tar.gz(r-4.7-x86_64)pwalign_1.9.1.tar.gz(r-4.6-arm64)pwalign_1.9.1.tar.gz(r-4.6-x86_64)
pwalign_1.9.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pwalign/json (API)
| # Install 'pwalign' in R: |
| install.packages('pwalign', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
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-1.9.1(bioc 3.24)pwalign-1.8.0(bioc 3.23)
alignmentsequencematchingsequencinggeneticsbioconductor-package
Last updated from:f1991c7341. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 248 | ||
| linux-devel-arm64 | NOTE | 247 | ||
| linux-devel-x86_64 | NOTE | 253 | ||
| source / vignettes | OK | 276 | ||
| linux-release-arm64 | NOTE | 257 | ||
| linux-release-x86_64 | NOTE | 273 | ||
| macos-release-arm64 | NOTE | 168 | ||
| macos-release-x86_64 | NOTE | 381 | ||
| macos-oldrel-arm64 | NOTE | 119 | ||
| macos-oldrel-x86_64 | NOTE | 520 | ||
| windows-devel | NOTE | 164 | ||
| windows-release | NOTE | 232 | ||
| windows-oldrel | NOTE | 222 | ||
| wasm-release | OK | 128 |
Exports:alignedalignedPatternalignedSubjectas.matrixcompareStringsconsensusMatrixcoveragedeletionenderrorSubstitutionMatricesindelinsertionmismatchmismatchSummarymismatchTablencharneditnindelnmatchnmismatchnucleotideSubstitutionMatrixpairwiseAlignmentPairwiseAlignmentsPairwiseAlignmentsSingleSubjectparallel_slot_namesparallelVectorNamespatternpidqualitySubstitutionMatricesscoreshowstartstringDistsubjectsummarytoStringtypeunalignedViewswidthwritePairwiseAlignments
Dependencies:BiocGenericsBiostringscrayongenericsIRangesS4VectorsSeqinfoXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Utility functions related to sequence alignment | align-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 objects | aligned 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 objects | class:InDel deletion deletion,InDel-method InDel InDel-class insertion insertion,InDel-method |
| Optimal Pairwise Alignment | pairwiseAlignment pairwiseAlignment,ANY,ANY-method pairwiseAlignment,ANY,QualityScaledXStringSet-method pairwiseAlignment,QualityScaledXStringSet,ANY-method pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method |
| PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects | aligned,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 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 file | PairwiseAlignments-io writePairwiseAlignments |
| Versions of bacteriophage phiX174 complete genome and sample short reads | phiX174Phage quPhiX174 srPhiX174 wtPhiX174 |
| Percent Sequence Identity | pid pid,PairwiseAlignments-method |
| Predefined scoring matrices | BLOSUM100 BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 PAM30 PAM40 PAM70 predefined_scoring_matrices |
| String Distance/Alignment Score Matrix | stringDist stringDist,character-method stringDist,QualityScaledXStringSet-method stringDist,XStringSet-method |
| Utilities to generate substitution matrices | errorSubstitutionMatrices nucleotideSubstitutionMatrix qualitySubstitutionMatrices substitution_matrices |
