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"aacost" ] }, { "page": "aaindex", "title": "List of 544 physicochemical and biological properties for the 20 amino-acids", "topics": [ "aaindex" ] }, { "page": "AAstat", "title": "To Get Some Protein Statistics", "topics": [ "AAstat" ] }, { "page": "acnucopen", "title": "open and close a remote access to an ACNUC database", "topics": [ "acnucclose", "acnucopen", "clientid", "quitacnuc" ] }, { "page": "al2bp", "title": "To Convert a forensic microsatellite allele name into its length in base pairs", "topics": [ "al2bp" ] }, { "page": "alllistranks", "title": "To get the count of existing lists and all their ranks on server", "topics": [ "alllistranks", "alr" ] }, { "page": "amb", "title": "Expansion of IUPAC nucleotide symbols", "topics": [ "amb" ] }, { "page": "AnoukResult", "title": "Expected numeric results for Ka and Ks computation", "topics": [ "AnoukResult" ] }, { "page": "as.alignment", "title": "Constructor for class alignment", "topics": [ "as.alignment" ] }, { "page": 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"closebank", "title": "To close a remote ACNUC database", "topics": [ "closebank" ] }, { "page": "clustal", "title": "Example of results obtained after a call to read.alignment", "topics": [ "clustal" ] }, { "page": "col2alpha", "title": "To use a standard color with an alpha transparency chanel", "topics": [ "col2alpha" ] }, { "page": "comp", "title": "complements a nucleic acid sequence", "topics": [ "comp" ] }, { "page": "computePI", "title": "To Compute the Theoretical Isoelectric Point", "topics": [ "computePI" ] }, { "page": "consensus", "title": "Consensus and profiles for sequence alignments", "topics": [ "con", "consensus" ] }, { "page": "count", "title": "Composition of dimer/trimer/etc oligomers", "topics": [ "count" ] }, { "page": "countfreelists", "title": "The number of free lists available and annotation lines in an ACNUC server", "topics": [ "cfl", "countfreelists" ] }, { "page": "countsubseqs", "title": "Number of subsequences in an ACNUC list", "topics": [ "countsubseqs", "css" ] }, { "page": "crelistfromclientdata", "title": "To create on server an ACNUC list from data lines sent by client", "topics": [ "clfcd", "crelistfromclientdata" ] }, { "page": "dia.bactgensize", "title": "Distribution of bacterial genome size from GOLD", "topics": [ "dia.bactgensize" ] }, { "page": "dinucl", "title": "Mean zscore on 242 complete bacterial chromosomes", "topics": [ "dinucl" ] }, { "page": "zscore", "title": "Statistical over- and under- representation of dinucleotides in a sequence", "topics": [ "rho", "zscore" ] }, { "page": "dist.alignment", "title": "Pairwise Distances from Aligned Protein or DNA/RNA Sequences", "topics": [ "dist.alignment" ] }, { "page": "dotchart.uco", "title": "Cleveland plot for codon usage tables", "topics": [ "dotchart.uco" ] }, { "page": "dotPlot", "title": "Dot Plot Comparison of two sequences", "topics": [ "dotPlot" ] }, { "page": "draw.oriloc", "title": "Graphical representation for nucleotide skews in prokaryotic chromosomes.", "topics": [ "draw.oriloc" ] }, { "page": "draw.rearranged.oriloc", "title": "Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.", "topics": [ "draw.rearranged.oriloc" ] }, { "page": "draw.recstat", "title": "Graphical representation of a recstat analysis.", "topics": [ "draw.recstat" ] }, { "page": "ec999", "title": "999 coding sequences from E. coli", "topics": [ "ec999" ] }, { "page": "ECH", "title": "Forensic Genetic Profile Allelic Ladder Raw Data", "topics": [ "ECH" ] }, { "page": "EXP", "title": "Vectors of coefficients to compute linear forms.", "topics": [ "EXP" ] }, { "page": "extract.breakpoints", "title": "Extraction of breakpoint positions on the rearranged nucleotide skews.", "topics": [ "extract.breakpoints" ] }, { "page": "extractseqs", "title": "To extract the sequences information of a sequence or a list of sequence in different formats", "topics": [ "exseq", "extractseqs" ] }, { "page": "fasta", "title": "Example of results obtained after a call to read.alignment", "topics": [ "fasta" ] }, { "page": "fastacc", "title": "Fast Allele in Common Count", "topics": [ "fastacc" ] }, { "page": "GC", "title": "Calculates the fractional G+C content of nucleic acid sequences.", "topics": [ "GC", "GC1", "GC2", "GC3", "GCpos" ] }, { "page": "gb2fasta", "title": "Conversion of GenBank file into fasta file", "topics": [ "gb2fasta" ] }, { "page": "gbk2g2", "title": "Conversion of a GenBank format file into a glimmer-like one", "topics": [ "gbk2g2" ] }, { "page": "gbk2g2.euk", "title": "Conversion of a GenBank format file into a glimmer-like one. Eukaryotic version.", "topics": [ "gbk2g2.euk" ] }, { "page": "gcO2", "title": "GC content and aerobiosis in bacteria", "topics": [ "gcO2" ] }, { "page": "gcT", "title": "GC content and temperature in bacteria", "topics": [ "gcT" ] }, { "page": "get.db.growth", "title": "Get the exponential growth of nucleic acid database content", "topics": [ "dia.db.growth", "get.db.growth" ] }, { "page": "getAnnot", "title": "Generic Function to get sequence annotations", "topics": [ "getAnnot", "getAnnot.default", "getAnnot.list", "getAnnot.logical", "getAnnot.qaw", "getAnnot.SeqAcnucWeb", "getAnnot.SeqFastaAA", "getAnnot.SeqFastadna", "readAnnots.socket" ] }, { "page": "getFrag", "title": "Generic function to extract sequence fragments", "topics": [ "getFrag", "getFrag.character", "getFrag.default", "getFrag.list", "getFrag.logical", "getFrag.qaw", "getFrag.SeqAcnucWeb", "getFrag.SeqFastaAA", "getFrag.SeqFastadna", "getFrag.SeqFrag" ] }, { "page": "getKeyword", "title": "Generic function to get keywords associated to sequences", "topics": [ "getKeyword", "getKeyword.default", "getKeyword.list", "getKeyword.logical", "getKeyword.qaw", "getKeyword.SeqAcnucWeb" ] }, { "page": "getLength", "title": "Generic function to get the length of sequences", "topics": [ "getLength", "getLength.character", "getLength.default", "getLength.list", "getLength.logical", "getLength.qaw", "getLength.SeqAcnucWeb", "getLength.SeqFastaAA", "getLength.SeqFastadna", "getLength.SeqFrag" ] }, { "page": "getlistrank", "title": "To get the rank of a list from its name", "topics": [ "getlistrank", "glr" ] }, { "page": "getliststate", "title": "Asks for information about an ACNUC list of specified rank", "topics": [ "getliststate", "gln", "gls" ] }, { "page": "getLocation", "title": "Generic function to get the location of subsequences on the parent sequence", "topics": [ "getLocation", "getLocation.default", "getLocation.list", "getLocation.logical", "getLocation.qaw", "getLocation.SeqAcnucWeb" ] }, { "page": "getName", "title": "Generic function to get the names of sequences", "topics": [ "getName", "getName.default", "getName.list", "getName.logical", "getName.qaw", "getName.SeqAcnucWeb", "getName.SeqFastaAA", "getName.SeqFastadna", "getName.SeqFrag" ] }, { "page": "getSequence", "title": "Generic function to get sequence data", "topics": [ "getSequence", "getSequence.character", "getSequence.default", "getSequence.list", "getSequence.logical", "getSequence.qaw", "getSequence.SeqAcnucWeb", "getSequence.SeqFastaAA", "getSequence.SeqFastadna", "getSequence.SeqFrag" ] }, { "page": "getTrans", "title": "Generic function to translate coding sequences into proteins", "topics": [ "getTrans", "getTrans.character", "getTrans.default", "getTrans.list", "getTrans.logical", "getTrans.qaw", "getTrans.SeqAcnucWeb", "getTrans.SeqFastadna", "getTrans.SeqFrag" ] }, { "page": "getType", "title": "To get available subsequence types in an opened ACNUC database", "topics": [ "getType" ] }, { "page": "gfrag", "title": "Extract sequence identified by name or by number from an ACNUC server", "topics": [ "gfrag" ] }, { "page": "ghelp", "title": "Get help from an ACNUC server", "topics": [ "ghelp" ] }, { "page": "gs500liz", "title": "GS500LIZ size standards", "topics": [ "gs500liz" ] }, { "page": "identifiler", "title": "Identifiler allele names", "topics": [ "identifiler" ] }, { "page": "isenum", "title": "Get the ACNUC number of a sequence from its name or accession number", "topics": [ "getAttributsocket", "getNumber.socket", "isenum", "isn" ] }, { "page": "JLO", "title": "Forensic Genetic Profile Raw Data", "topics": [ "JLO" ] }, { "page": "kaks", "title": "Ka and Ks, also known as dn and ds, computation", "topics": [ "kaks" ] }, { "page": "kaks-torture", "title": "Expected numeric results for Ka and Ks in extreme cases", "topics": [ "kaksTorture" ] }, { "page": "knowndbs", "title": "Description of databases known by an ACNUC server", "topics": [ "kdb", "knowndbs" ] }, { "page": "lseqinr", "title": "To see what's inside the package seqinr", "topics": [ "lseqinr" ] }, { "page": "m16j", "title": "Fragment of the E. coli chromosome", "topics": [ "m16j" ] }, { "page": "mase", "title": "Example of results obtained after a call to read.alignment", "topics": [ "mase" ] }, { "page": "modifylist", "title": "Modification of an ACNUC list", "topics": [ "modifylist" ] }, { "page": "move", "title": "Rename an R object", "topics": [ "move", "mv" ] }, { "page": "msf", "title": "Example of results obtained after a call to read.alignment", "topics": [ "msf" ] }, { "page": "n2s", "title": "function to convert the numeric encoding of a DNA sequence into a vector of characters", "topics": [ "n2s" ] }, { "page": "oriloc", "title": "Prediction of origin and terminus of replication in bacteria.", "topics": [ "oriloc" ] }, { "page": "parser.socket", "title": "Utility function to parse answers from an ACNUC server", "topics": [ "parser.socket" ] }, { "page": "peakabif", "title": "Extraction of Peak locations, Heights and Surfaces from ABIF data", "topics": [ "peakabif" ] }, { "page": "permutation", "title": "Sequence permutation according to several different models", "topics": [ "permutation" ] }, { "page": "phylip", "title": "Example of results obtained after a call to read.alignment", "topics": [ "phylip" ] }, { "page": "pK", "title": "pK values for the side chain of charged amino acids from various sources", "topics": [ "pK" ] }, { "page": "plot.SeqAcnucWeb", "title": "To Plot Subsequences on the Parent Sequence", "topics": [ "plot.SeqAcnucWeb" ] }, { "page": "plotabif", "title": "Electrophoregram plot for ABIF data", "topics": [ "plotabif" ] }, { "page": "plotladder", "title": "Simple plot of an allelic ladder from ABIF data", "topics": [ "plotladder" ] }, { "page": "plotPanels", "title": "Representation of Amplicon Size Ranges of a STR kit.", "topics": [ "plotPanels" ] }, { "page": "pmw", "title": "Protein Molecular Weight", "topics": [ "pmw" ] }, { "page": "prepgatannots", "title": "Select annotation lines in an ACNUC database", "topics": [ "pga", "prepgetannots" ] }, { "page": "prettyseq", "title": "Text representation of a sequence from an ACNUC server", "topics": [ "prettyseq" ] }, { "page": "print.qaw", "title": "Print method for objects from class qaw", "topics": [ "print.qaw" ] }, { "page": "print.SeqAcnucWeb", "title": "Print method for objects from class SeqAcnucWeb", "topics": [ "print.SeqAcnucWeb" ] }, { "page": "prochlo", "title": "Zscore on three strains of Prochlorococcus marinus", "topics": [ "prochlo" ] }, { "page": "query", "title": "To get a list of sequence names from an ACNUC data base located on the web", "topics": [ "query" ] }, { "page": "read.abif", "title": "Read ABIF formatted files", "topics": [ "read.abif" ] }, { "page": "read.alignment", "title": "Read aligned sequence files in mase, clustal, phylip, fasta or msf format", "topics": [ "read.alignment" ] }, { "page": "read.fasta", "title": "read FASTA formatted files", "topics": [ "FASTA", "read.fasta", "readfasta" ] }, { "page": "readBins", "title": "Import GenMapper Bins configuration file", "topics": [ "readBins" ] }, { "page": "readfirstrec", "title": "Low level function to get the record count of the specified ACNUC index file", "topics": [ "readfirstrec" ] }, { "page": "readPanels", "title": "Import GenMapper Panels configuration file", "topics": [ "readPanels" ] }, { "page": "readsmj", "title": "Low level function to read ACNUC SMJYT index files", "topics": [ "readsmj" ] }, { "page": "rearranged.oriloc", "title": "Detection of replication-associated effects on base composition asymmetry in prokaryotic chromosomes.", "topics": [ "rearranged.oriloc" ] }, { "page": "recstat", "title": "Prediction of Coding DNA Sequences.", "topics": [ "recstat" ] }, { "page": "residuecount", "title": "Total number of residues in an ACNUC list", "topics": [ "residuecount" ] }, { "page": "revaligntest", "title": "Three aligned nucleic acid sequences", "topics": [ "revaligntest" ] }, { "page": "reverse.align", "title": "Reverse alignment - from protein sequence alignment to nucleic sequence alignment", "topics": [ "reverse.align" ] }, { "page": "rot13", "title": "Ergheaf gur EBG-13 pvcurevat bs n fgevat", "topics": [ "rot13" ] }, { "page": "s2c", "title": "conversion of a string into a vector of chars", "topics": [ "s2c" ] }, { "page": "s2n", "title": "simple numerical encoding of a DNA sequence.", "topics": [ "s2n" ] }, { "page": "savelist", "title": "Save sequence names or accession numbers into a file", "topics": [ "savelist" ] }, { "page": "SeqAcnucWeb", "title": "Sequence coming from a remote ACNUC data base", "topics": [ "as.SeqAcnucWeb", "is.SeqAcnucWeb", "SeqAcnucWeb" ] }, { "page": "SeqFastaAA", "title": "AA sequence in Fasta Format", "topics": [ "as.SeqFastaAA", "is.SeqFastaAA", "SeqFastaAA", "summary.SeqFastaAA" ] }, { "page": "SeqFastadna", "title": "Class for DNA sequence in Fasta Format", "topics": [ "as.SeqFastadna", "is.SeqFastadna", "SeqFastadna", "summary.SeqFastadna" ] }, { "page": "SeqFrag", "title": "Class for sub-sequences", "topics": [ "as.SeqFrag", "is.SeqFrag", "SeqFrag" ] }, { "page": "SEQINR.UTIL", "title": "utility data for seqinr", "topics": [ "SEQINR.UTIL" ] }, { "page": "setlistname", "title": "Sets the name of an ACNUC list identified by its rank", "topics": [ "setlistname" ] }, { "page": "splitseq", "title": "split a sequence into sub-sequences", "topics": [ "splitseq" ] }, { "page": "stresc", "title": "Utility function to escape LaTeX special characters present in a string", "topics": [ "stresc" ] }, { "page": "stutterabif", "title": "Stutter ratio estimation", "topics": [ "stutterabif" ] }, { "page": "swap", "title": "Exchange two R objects", "topics": [ "swap" ] }, { "page": "syncodons", "title": "Synonymous codons", "topics": [ "syncodons" ] }, { "page": "synsequence", "title": "Random synonymous coding sequence generation", "topics": [ "synsequence" ] }, { "page": "tablecode", "title": "to plot genetic code as in textbooks", "topics": [ "tablecode" ] }, { "page": "test.co.recstat", "title": "Tests if regions located between Stop codons contain putative CDSs.", "topics": [ "test.co.recstat" ] }, { "page": "test.li.recstat", "title": "Tests if regions located between Stop codons contain putative CDSs.", "topics": [ "test.li.recstat" ] }, { "page": "toyaa", "title": "A toy example of amino-acid counts in three proteins", "topics": [ "toyaa" ] }, { "page": "toycodon", "title": "A toy example of codon counts in three coding sequences", "topics": [ "toycodon" ] }, { "page": "translate", "title": "Translate nucleic acid sequences into proteins", "topics": [ "translate" ] }, { "page": "trimSpace", "title": "Trim leading and/or trailing spaces in strings", "topics": [ "trimSpace" ] }, { "page": "uco", "title": "Codon usage indices", "topics": [ "rscu", "uco" ] }, { "page": "ucoweight", "title": "Weight of each synonymous codon", "topics": [ "ucoweight" ] }, { "page": "waterabs", "title": "Light absorption by the water column", "topics": [ "waterabs" ] }, { "page": "where.is.this.acc", "title": "Scans databases for a given sequence accession number", "topics": [ "where.is.this.acc" ] }, { "page": "words", "title": "To get all words from an alphabet.", "topics": [ "words" ] }, { "page": "words.pos", "title": "Positions of possibly degenerated motifs within sequences", "topics": [ "words.pos" ] }, { "page": "write.fasta", "title": "Write sequence(s) into a file in fasta format", "topics": [ "write.fasta" ] } ], "_readme": "https://github.com/lbbe-software/seqinr/raw/HEAD/README.md", "_rundeps": [ "ade4", "lattice", "MASS", "nlme", "pixmap", "Rcpp", "RcppArmadillo", "segmented", "sp" ], "_sysdeps": [ { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" } ], 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