GenomAutomorphism Overview | Installing GenomAutomorphism | Automorphisms | Load the R libraries | Read the alignment FASTA and encode the sequences | Group representations | "Dual" genetic-code cubes | Automorphisms on $\mathbb{Z}_{64}$ | Automorphisms between whole genomes of SARS-CoV-2 related coronaviruses | Bar plot automorphism distribution by cubes | Grouping automorphism by automorphism's coefficients. Types of mutations | Conserved and non-conserved regions | Conserved regions | Automorphisms on $\mathbb{Z}_{125}$ | Automorphisms on the Genetic-code Cube Representation on GF(5) | Grouping automorphism by automorphism's coefficients | References | Session info
Package: GenomAutomorphism 1.15.0
Robersy Sanchez
GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations
This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.
Authors:
GenomAutomorphism_1.15.0.tar.gz
GenomAutomorphism_1.15.0.zip(r-4.7)GenomAutomorphism_1.15.0.zip(r-4.6)GenomAutomorphism_1.15.0.zip(r-4.5)
GenomAutomorphism_1.15.0.tgz(r-4.6-any)GenomAutomorphism_1.15.0.tgz(r-4.5-any)
GenomAutomorphism_1.15.0.tar.gz(r-4.7-any)GenomAutomorphism_1.15.0.tar.gz(r-4.6-any)
GenomAutomorphism_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomAutomorphism/json (API)
| # Install 'GenomAutomorphism' in R: |
| install.packages('GenomAutomorphism', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/genomaths/genomautomorphism/issues
Datasets:
- aaindex1 - List of 571 Amino Acid Physicochemical Indexes from AAindex Database
- aaindex2 - List of 94 Amino Acid Matrices from AAindex
- aaindex3 - Statistical protein contact potentials matrices from AAindex ver.9.2
- aln - Simulated 'DNAStringSet' class object
- autby_coef - Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients
- autm - Automorphisms between DNA Sequences from two COVID-19 genomes
- autm_3d - Automorphisms between DNA Sequences from two COVID-19 genomes
- autm_z125 - Automorphisms between DNA Sequences from two COVID-19 genomes
- brca1_aln - Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
- brca1_aln2 - Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
- brca1_autm - Automorphisms between DNA Sequences from Primate BRCA1 Genes
- brca1_autm2 - Automorphisms between DNA Sequences from Primate BRCA1 Genes
- cdm_z64 - Codon Distance Matrices for the Standard Genetic Code on Z4
- covid_aln - Pairwise Sequence Alignment (MSA) of COVID-19 genomes.
- covid_autm - Automorphisms between DNA Sequences from two COVID-19 genomes
- cyc_aln - Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C
- cyc_autm - Automorphisms between DNA Sequences from Primate Cytochrome C Genes
- dna_phyche - Some Physicochemical Properties of DNA bases
On BioConductor:GenomAutomorphism-1.15.0(bioc 3.24)GenomAutomorphism-1.14.0(bioc 3.23)
mathematicalbiologycomparativegenomicsfunctionalgenomicsmultiplesequencealignmentwholegenomegenetic-codegenetic-code-algebragenomegenome-algebra
Last updated from:34d8013455. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 173 | ||
| linux-devel-x86_64 | WARNING | 357 | ||
| source / vignettes | OK | 259 | ||
| linux-release-x86_64 | WARNING | 290 | ||
| macos-release-arm64 | WARNING | 234 | ||
| macos-oldrel-arm64 | WARNING | 208 | ||
| windows-devel | WARNING | 263 | ||
| windows-release | WARNING | 327 | ||
| windows-oldrel | WARNING | 301 | ||
| wasm-release | OK | 144 |
Exports:aa_indexaa_mutmataa_phychem_indexAAMultipleAlignmentAAStringSetaminoacid_distas.AutomorphismListas.listaut3Dautomorphism_bycoefautomorphism_probautomorphismByRangesautomorphismsautZ125autZ5autZ64base_coordbase_matrixbase_seq2string_setbase2codonbase2intcodon_coordcodon_distcodon_dist_matrixcodon_matrixCodonMatrixcolMeans2colSdscolSums2colVarsconserved_regionscoordListdna_phychemDNAMultipleAlignmentDNAStringSetendend<-GENETIC_CODE_TABLEget_coordget_mutscoregetAutomorphismsgetGeneticCodeGRangesListGRangesMatrixSeqListCodonMatrixmakeGRangesFromDataFramematricesMatrixSeqmcolsmcols<-modmodeqmodlinmodlineqmodqmut_typepeptide_phychem_indexreadDNAMultipleAlignmentrowMeans2rowSdsrowSums2rowVarsseq2grangesseqrangesseqRangessetValidity2showslapplysortByChromAndEndsortByChromAndStartstartstart<-str2chrstr2digstrandstrand<-subseqtranslatetranslationunmaskedwidth
Dependencies:BHBiocGenericsBiocParallelBiostringsclicodetoolscpp11crayondata.tabledoParalleldplyrforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesglueIRangesiteratorslambda.rlifecyclemagrittrmatrixStatsnumberspillarpkgconfigR6rlangS4VectorsSeqinfosnowtibbletidyselectutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Amino acid mutation matrix | aa_index aa_mutmat aa_phychem_index |
| List of 571 Amino Acid Physicochemical Indexes from AAindex Database | aaindex1 |
| List of 94 Amino Acid Matrices from AAindex | aaindex2 |
| Statistical protein contact potentials matrices from AAindex ver.9.2 | aaindex3 |
| Simulated 'DNAStringSet' class object | aln |
| Distance Between Aminoacids in Terms of Codon Distance | aminoacid_dist aminoacid_dist,AAStringSet,ANY-method aminoacid_dist,character,character-method aminoacid_dist,CodonGroup_OR_Automorphisms,ANY-method aminoacid_dist,DNAStringSet,ANY-method |
| Methods for AutomorphismList-class Objects | as.AutomorphismList as.AutomorphismList,GRangesList,GRanges_OR_NULL-method as.AutomorphismList,list,GRanges_OR_NULL-method |
| Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5^3. | aut3D |
| Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients | autby_coef |
| Automorphisms between DNA Sequences from two COVID-19 genomes | autm |
| Automorphisms between DNA Sequences from two COVID-19 genomes | autm_3d |
| Automorphisms between DNA Sequences from two COVID-19 genomes | autm_z125 |
| Autmorphism Grouping by Coefficient | automorphism_bycoef automorphism_bycoef,Automorphism-method automorphism_bycoef,AutomorphismList-method |
| Autmorphism Probability | automorphism_prob automorphism_prob,AutomorphismByCoef-method automorphism_prob,AutomorphismByCoefList-method |
| Get the automorphisms by ranges. | automorphismByRanges automorphismByRanges,Automorphism-method automorphismByRanges,AutomorphismList-method |
| Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group. | automorphisms automorphisms,DNAStringSet_OR_NULL-method |
| Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z125. | autZ125 |
| Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5. | autZ5 |
| Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z64. | autZ64 |
| DNA Sequences Methods | base_coord base_coord,DNAStringSet_OR_NULL-method base_matrix base_matrix,DNAStringSet_OR_NULL-method base_methods base_seq2string_set base_seq2string_set,BaseSeq-method seq2granges seq2granges,DNAStringSet_OR_NULL-method |
| Split a DNA sequence into codons | base2codon base2codon,character-method base2codon,DNAMultipleAlignment-method base2codon,DNAStringSet-method |
| Replace bases with integers from Z4 and Z5 | base2int base2int,character-method base2int,data.frame-method |
| Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes. | brca1_aln |
| Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes. | brca1_aln2 |
| Automorphisms between DNA Sequences from Primate BRCA1 Genes | brca1_autm |
| Automorphisms between DNA Sequences from Primate BRCA1 Genes | brca1_autm2 |
| Codon Distance Matrices for the Standard Genetic Code on Z4 | cdm_z64 |
| Codon coordinates on a given a given Abelian group representation. | codon_coord codon_coord,BaseGroup-method codon_coord,DNAStringSet_OR_NULL-method codon_coord,matrix_OR_data_frame-method |
| Weighted Manhattan Distance Between Codons | codon_dist codon_dist,character-method codon_dist,CodonGroup_OR_Automorphisms-method codon_dist,DNAStringSet-method |
| Compute Codon Distance Matrix | codon_dist_matrix |
| Codon Coordinate Matrix | codon_matrix codon_matrix,BaseSeqMatrix-method codon_matrix,DNAMultipleAlignment-method codon_matrix,DNAStringSet-method |
| Conserved and Non-conserved Regions from a MSA | conserved_regions conserved_regions,Automorphism-method conserved_regions,AutomorphismByCoef-method conserved_regions,AutomorphismByCoefList-method conserved_regions,AutomorphismList-method |
| Pairwise Sequence Alignment (MSA) of COVID-19 genomes. | covid_aln |
| Automorphisms between DNA Sequences from two COVID-19 genomes | covid_autm |
| Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C | cyc_aln |
| Automorphisms between DNA Sequences from Primate Cytochrome C Genes | cyc_autm |
| Some Physicochemical Properties of DNA bases | dna_phyche |
| DNA numerical matrix | dna_phychem dna_phychem,character-method dna_phychem,DNAStringSet_OR_DNAMultipleAlignment-method |
| DNA base/codon sequence and coordinates represented on a given Abelian group. | get_coord get_coord,BaseGroup_OR_CodonGroup-method get_coord,DNAStringSet_OR_NULL-method |
| Get Mutation Score from an AAindex or a Mutation/Distance Matrix | get_mutscore get_mutscore,BaseSeq,missing-method get_mutscore,character,character-method get_mutscore,DNAMultipleAlignment,missing-method get_mutscore,DNAStringSet,missing-method |
| Get Automorphisms | getAutomorphisms getAutomorphisms,AutomorphismList-method getAutomorphisms,DataFrame_OR_data.frame-method getAutomorphisms,list-method |
| Get the Coordinate Representation from DNA Sequences on Specified Abelian Group | matrices matrices,CodonSeq-method matrices,DNAStringSet_OR_NULL-method matrices,MatrixList-method |
| Modulo Operation | '%%' mod mod,matrix,numeric-method modulo |
| Modular System of Linear Equation Solver (MLE) | modlineq |
| Classification of DNA base mutations | mut_type |
| Amino acid numerical matrix | peptide_phychem_index peptide_phychem_index,character-method peptide_phychem_index,DNAStringSet_OR_DNAMultipleAlignment-method |
| Get DNA sequence Ranges and Coordinates representation on a given Abelian Group | seqranges seqranges,CodonSeq-method seqranges,DNAStringSet_OR_NULL-method |
| Apply a function over a list-like object preserving its attributes | slapply |
| Sorting 'GRanges-class' objects | sortByChromAndEnd sortByChromAndStart |
| String to Character | str2chr str2chr,character-method str2chr,list-method |
| String to Digits | str2dig str2dig,character-method str2dig,list-method |
| Translation of DNA/RNA sequences | translation translation,BioString-method translation,character-method |
