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
get.ncbi                Bacterial complete genome data from ncbi ftp
                        site
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
