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