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