Sequence coming from a remote ACNUC data base
utility data for seqinr
Forensic Genetic Profile Raw Data
Expected numeric results for Ka and Ks computation
Calculates the fractional G+C content of nucleic acid sequences.
Vectors of coefficients to compute linear forms.
Forensic Genetic Profile Allelic Ladder Raw Data
To Get Some Protein Statistics
Class for DNA sequence in Fasta Format
AA sequence in Fasta Format
Class for sub-sequences
To get the count of existing lists and all their ranks on server
To Convert a forensic microsatellite allele name into its length in base pairs
Base composition in ssDNA for 7 bacterial DNA
as.matrix.alignment
Draws a circle
Returns a socket to the last opened database
Converts amino-acid three-letter code into the one-letter one
To select a database structured under ACNUC and located on the web
Codon Adaptation Index (CAI) w tables
conversion of a vector of chars into a string
open and close a remote access to an ACNUC database
List of 544 physicochemical and biological properties for the 20 amino-acids
To close a remote ACNUC database
Codon Adaptation Index
To Compute the Theoretical Isoelectric Point
Expansion of IUPAC nucleotide symbols
Estimation of baseline value
Computing an IUPAC nucleotide symbol
Constructor for class alignment
Consensus and profiles for sequence alignments
Example of results obtained after a call to read.alignment
Graphical representation for nucleotide skews in
prokaryotic chromosomes.
complements a nucleic acid sequence
To use a standard color with an alpha transparency chanel
Cleveland plot for codon usage tables
Conversion of a GenBank format file into a glimmer-like one
To create on server an ACNUC list from data lines sent by client
Distribution of bacterial genome size from GOLD
Number of subsequences in an ACNUC list
Mean zscore on 242 complete bacterial chromosomes
Graphical representation for rearranged nucleotide skews in
prokaryotic chromosomes.
Dot Plot Comparison of two sequences
Pairwise Distances from Aligned Protein or DNA/RNA Sequences
The number of free lists available and annotation lines in an ACNUC server
Composition of dimer/trimer/etc oligomers
Graphical representation of a recstat analysis.
Get the exponential growth of nucleic acid database content
To get the rank of a list from its name
Fast Allele in Common Count
Asks for information about an ACNUC list of specified rank
Conversion of GenBank file into fasta file
Generic Function to get sequence annotations
GC content and temperature in bacteria
GC content and aerobiosis in bacteria
Generic function to get the names of sequences
Generic function to extract sequence fragments
Generic function to get keywords associated to sequences
Sequence permutation according to several different models
Extraction of Peak locations, Heights and Surfaces from ABIF data
Simple plot of an allelic ladder from ABIF data
Protein Molecular Weight
To get available subsequence types in an opened ACNUC database
Generic function to translate coding sequences into proteins
Generic function to get sequence data
Conversion of a GenBank format file into a glimmer-like
one. Eukaryotic version.
Ka and Ks, also known as dn and ds, computation
Description of databases known by an ACNUC server
To extract the sequences information of a sequence or a list of sequence in different formats
Expected numeric results for Ka and Ks in extreme cases
function to convert the numeric encoding of a DNA sequence
into a vector of characters
Get the ACNUC number of a sequence from its name or accession number
Extract sequence identified by name or by number from an ACNUC server
Example of results obtained after a call to read.alignment
pK values for the side chain of charged amino acids from various sources
Get help from an ACNUC server
GS500LIZ size standards
Prediction of origin and terminus of replication in bacteria.
Prediction of Coding DNA Sequences.
Rename an R object
Identifiler allele names
Total number of residues in an ACNUC list
Detection of replication-associated effects on base composition asymmetry in
prokaryotic chromosomes.
Low level function to read ACNUC SMJYT index files
Example of results obtained after a call to read.alignment
To Plot Subsequences on the Parent Sequence
Converts amino-acid one-letter code into the three-letter one
Aerobic cost of amino-acids in Escherichia coli and G+C classes
Example of results obtained after a call to read.alignment
999 coding sequences from E. coli
Extraction of breakpoint positions on the
rearranged nucleotide skews.
Representation of Amplicon Size Ranges of a STR kit.
Text representation of a sequence from an ACNUC server
Zscore on three strains of Prochlorococcus marinus
To get a list of sequence names from an ACNUC data base located on the web
Select annotation lines in an ACNUC database
Read ABIF formatted files
Electrophoregram plot for ABIF data
Generic function to get the length of sequences
Read aligned sequence files in mase, clustal, phylip, fasta or msf format
Generic function to get the location of subsequences on the parent sequence
simple numerical encoding of a DNA sequence.
To see what's inside the package seqinr
Save sequence names or accession numbers into a file
Utility function to parse answers from an ACNUC server
Translate nucleic acid sequences into proteins
A toy example of amino-acid counts in three proteins
A toy example of codon counts in three coding sequences
Tests if regions located between Stop codons contain putative CDSs.
Print method for objects from class SeqAcnucWeb
Synonymous codons
Statistical over- and under- representation of dinucleotides in a
sequence
Three aligned nucleic acid sequences
Random synonymous coding sequence generation
Fragment of the E. coli chromosome
read FASTA formatted files
Ergheaf gur EBG-13 pvcurevat bs n fgevat
Import GenMapper Bins configuration file
Print method for objects from class qaw
conversion of a string into a vector of chars
Modification of an ACNUC list
Example of results obtained after a call to read.alignment
Import GenMapper Panels configuration file
Light absorption by the water column
Weight of each synonymous codon
Low level function to get the record count of the specified ACNUC
index file
Stutter ratio estimation
Reverse alignment - from protein sequence alignment to nucleic sequence alignment
to plot genetic code as in textbooks
Exchange two R objects
Biological Sequences Retrieval and Analysis
Scans databases for a given sequence accession number
To get all words from an alphabet.
Tests if regions located between Stop codons contain putative CDSs.
Utility function to escape LaTeX special characters present in a string
Sets the name of an ACNUC list identified by its rank
split a sequence into sub-sequences
Trim leading and/or trailing spaces in strings
Codon usage indices
Positions of possibly degenerated motifs within sequences
Write sequence(s) into a file in fasta format