AAstat To Get Some Protein Statistics AnoukResult Expected numeric results for Ka and Ks computation ECH Forensic Genetic Profile Allelic Ladder Raw Data EXP Vectors of coefficients to compute linear forms. GC Calculates the fractional G+C content of nucleic acid sequences. JLO Forensic Genetic Profile Raw Data SEQINR.UTIL utility data for seqinr SeqAcnucWeb Sequence coming from a remote ACNUC data base SeqFastaAA AA sequence in Fasta Format SeqFastadna Class for DNA sequence in Fasta Format SeqFrag Class for sub-sequences a Converts amino-acid three-letter code into the one-letter one aaa Converts amino-acid one-letter code into the three-letter one aacost Aerobic cost of amino-acids in Escherichia coli and G+C classes aaindex List of 544 physicochemical and biological properties for the 20 amino-acids acnucopen open and close a remote access to an ACNUC database al2bp To Convert a forensic microsatellite allele name into its length in base pairs alllistranks To get the count of existing lists and all their ranks on server amb Expansion of IUPAC nucleotide symbols as.alignment Constructor for class alignment as.matrix.alignment as.matrix.alignment autosocket Returns a socket to the last opened database baselineabif Estimation of baseline value bma Computing an IUPAC nucleotide symbol c2s conversion of a vector of chars into a string cai Codon Adaptation Index caitab Codon Adaptation Index (CAI) w tables chargaff Base composition in ssDNA for 7 bacterial DNA choosebank To select a database structured under ACNUC and located on the web circle Draws a circle closebank To close a remote ACNUC database clustal Example of results obtained after a call to read.alignment col2alpha To use a standard color with an alpha transparency chanel comp complements a nucleic acid sequence computePI To Compute the Theoretical Isoelectric Point consensus Consensus and profiles for sequence alignments count Composition of dimer/trimer/etc oligomers countfreelists The number of free lists available and annotation lines in an ACNUC server countsubseqs Number of subsequences in an ACNUC list crelistfromclientdata To create on server an ACNUC list from data lines sent by client dia.bactgensize Distribution of bacterial genome size from GOLD dinucl Mean zscore on 242 complete bacterial chromosomes dist.alignment Pairwise Distances from Aligned Protein or DNA/RNA Sequences dotPlot Dot Plot Comparison of two sequences dotchart.uco Cleveland plot for codon usage tables draw.oriloc Graphical representation for nucleotide skews in prokaryotic chromosomes. draw.rearranged.oriloc Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes. draw.recstat Graphical representation of a recstat analysis. ec999 999 coding sequences from E. coli extract.breakpoints Extraction of breakpoint positions on the rearranged nucleotide skews. extractseqs To extract the sequences information of a sequence or a list of sequence in different formats fasta Example of results obtained after a call to read.alignment fastacc Fast Allele in Common Count gb2fasta Conversion of GenBank file into fasta file gbk2g2 Conversion of a GenBank format file into a glimmer-like one gbk2g2.euk Conversion of a GenBank format file into a glimmer-like one. Eukaryotic version. gcO2 GC content and aerobiosis in bacteria gcT GC content and temperature in bacteria get.db.growth Get the exponential growth of nucleic acid database content getAnnot Generic Function to get sequence annotations getFrag Generic function to extract sequence fragments getKeyword Generic function to get keywords associated to sequences getLength Generic function to get the length of sequences getLocation Generic function to get the location of subsequences on the parent sequence getName Generic function to get the names of sequences getSequence Generic function to get sequence data getTrans Generic function to translate coding sequences into proteins getType To get available subsequence types in an opened ACNUC database getlistrank To get the rank of a list from its name getliststate Asks for information about an ACNUC list of specified rank gfrag Extract sequence identified by name or by number from an ACNUC server ghelp Get help from an ACNUC server gs500liz GS500LIZ size standards identifiler Identifiler allele names isenum Get the ACNUC number of a sequence from its name or accession number kaks Ka and Ks, also known as dn and ds, computation kaksTorture Expected numeric results for Ka and Ks in extreme cases knowndbs Description of databases known by an ACNUC server lseqinr To see what's inside the package seqinr m16j Fragment of the E. coli chromosome mase Example of results obtained after a call to read.alignment modifylist Modification of an ACNUC list move Rename an R object msf Example of results obtained after a call to read.alignment n2s function to convert the numeric encoding of a DNA sequence into a vector of characters oriloc Prediction of origin and terminus of replication in bacteria. pK pK values for the side chain of charged amino acids from various sources parser.socket Utility function to parse answers from an ACNUC server peakabif Extraction of Peak locations, Heights and Surfaces from ABIF data permutation Sequence permutation according to several different models phylip Example of results obtained after a call to read.alignment plot.SeqAcnucWeb To Plot Subsequences on the Parent Sequence plotPanels Representation of Amplicon Size Ranges of a STR kit. plotabif Electrophoregram plot for ABIF data plotladder Simple plot of an allelic ladder from ABIF data pmw Protein Molecular Weight prepgetannots Select annotation lines in an ACNUC database prettyseq Text representation of a sequence from an ACNUC server print.SeqAcnucWeb Print method for objects from class SeqAcnucWeb print.qaw Print method for objects from class qaw prochlo Zscore on three strains of Prochlorococcus marinus query To get a list of sequence names from an ACNUC data base located on the web read.abif Read ABIF formatted files read.alignment Read aligned sequence files in mase, clustal, phylip, fasta or msf format read.fasta read FASTA formatted files readBins Import GenMapper Bins configuration file readPanels Import GenMapper Panels configuration file readfirstrec Low level function to get the record count of the specified ACNUC index file readsmj Low level function to read ACNUC SMJYT index files rearranged.oriloc Detection of replication-associated effects on base composition asymmetry in prokaryotic chromosomes. recstat Prediction of Coding DNA Sequences. residuecount Total number of residues in an ACNUC list revaligntest Three aligned nucleic acid sequences reverse.align Reverse alignment - from protein sequence alignment to nucleic sequence alignment rho Statistical over- and under- representation of dinucleotides in a sequence rot13 Ergheaf gur EBG-13 pvcurevat bs n fgevat s2c conversion of a string into a vector of chars s2n simple numerical encoding of a DNA sequence. savelist Save sequence names or accession numbers into a file seqinr-package Biological Sequences Retrieval and Analysis setlistname Sets the name of an ACNUC list identified by its rank splitseq split a sequence into sub-sequences stresc Utility function to escape LaTeX special characters present in a string stutterabif Stutter ratio estimation swap Exchange two R objects syncodons Synonymous codons synsequence Random synonymous coding sequence generation tablecode to plot genetic code as in textbooks test.co.recstat Tests if regions located between Stop codons contain putative CDSs. test.li.recstat Tests if regions located between Stop codons contain putative CDSs. toyaa A toy example of amino-acid counts in three proteins toycodon A toy example of codon counts in three coding sequences translate Translate nucleic acid sequences into proteins trimSpace Trim leading and/or trailing spaces in strings uco Codon usage indices ucoweight Weight of each synonymous codon waterabs Light absorption by the water column where.is.this.acc Scans databases for a given sequence accession number words To get all words from an alphabet. words.pos Positions of possibly degenerated motifs within sequences write.fasta Write sequence(s) into a file in fasta format