seqinr

To Get Some Protein Statistics

Expected numeric results for Ka and Ks computation

Forensic Genetic Profile Allelic Ladder Raw Data

Vectors of coefficients to compute linear forms.

Calculates the fractional G+C content of nucleic acid sequences.

Forensic Genetic Profile Raw Data

utility data for seqinr

Sequence coming from a remote ACNUC data base

AA sequence in Fasta Format

Class for DNA sequence in Fasta Format

Class for sub-sequences

Converts amino-acid three-letter code into the one-letter one

Converts amino-acid one-letter code into the three-letter one

Aerobic cost of amino-acids in Escherichia coli and G+C classes

List of 544 physicochemical and biological properties for the 20 amino-acids

open and close a remote access to an ACNUC database

To Convert a forensic microsatellite allele name into its length in base pairs

To get the count of existing lists and all their ranks on server

Expansion of IUPAC nucleotide symbols

Constructor for class alignment

as.matrix.alignment

Returns a socket to the last opened database

Estimation of baseline value

Computing an IUPAC nucleotide symbol

conversion of a vector of chars into a string

Codon Adaptation Index

Codon Adaptation Index (CAI) w tables

Base composition in ssDNA for 7 bacterial DNA

To select a database structured under ACNUC and located on the web

Draws a circle

To close a remote ACNUC database

Example of results obtained after a call to read.alignment

To use a standard color with an alpha transparency chanel

complements a nucleic acid sequence

To Compute the Theoretical Isoelectric Point

Consensus and profiles for sequence alignments

Composition of dimer/trimer/etc oligomers

The number of free lists available and annotation lines in an ACNUC server

Number of subsequences in an ACNUC list

To create on server an ACNUC list from data lines sent by client

Distribution of bacterial genome size from GOLD

Mean zscore on 242 complete bacterial chromosomes

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Dot Plot Comparison of two sequences

Cleveland plot for codon usage tables

Graphical representation for nucleotide skews in prokaryotic chromosomes.

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Graphical representation of a recstat analysis.

999 coding sequences from E. coli

Extraction of breakpoint positions on the rearranged nucleotide skews.

To extract the sequences information of a sequence or a list of sequence in different formats

Example of results obtained after a call to read.alignment

Fast Allele in Common Count

Conversion of GenBank file into fasta file

Conversion of a GenBank format file into a glimmer-like one

Conversion of a GenBank format file into a glimmer-like one. Eukaryotic version.

GC content and aerobiosis in bacteria

GC content and temperature in bacteria

Get the exponential growth of nucleic acid database content

Generic Function to get sequence annotations

Generic function to extract sequence fragments

Generic function to get keywords associated to sequences

Generic function to get the length of sequences

Generic function to get the location of subsequences on the parent sequence

Generic function to get the names of sequences

Generic function to get sequence data

Generic function to translate coding sequences into proteins

To get available subsequence types in an opened ACNUC database

To get the rank of a list from its name

Asks for information about an ACNUC list of specified rank

Extract sequence identified by name or by number from an ACNUC server

Get help from an ACNUC server

GS500LIZ size standards

Identifiler allele names

Get the ACNUC number of a sequence from its name or accession number

Ka and Ks, also known as dn and ds, computation

Expected numeric results for Ka and Ks in extreme cases

Description of databases known by an ACNUC server

To see what's inside the package seqinr

Fragment of the E. coli chromosome

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

function to convert the numeric encoding of a DNA sequence into a vector of characters

Prediction of origin and terminus of replication in bacteria.

pK values for the side chain of charged amino acids from various sources

Utility function to parse answers from an ACNUC server

Extraction of Peak locations, Heights and Surfaces from ABIF data

Sequence permutation according to several different models

Example of results obtained after a call to read.alignment

To Plot Subsequences on the Parent Sequence

Representation of Amplicon Size Ranges of a STR kit.

Electrophoregram plot for ABIF data

Simple plot of an allelic ladder from ABIF data

Protein Molecular Weight

Select annotation lines in an ACNUC database

Text representation of a sequence from an ACNUC server

Print method for objects from class SeqAcnucWeb

Print method for objects from class qaw

Zscore on three strains of Prochlorococcus marinus

To get a list of sequence names from an ACNUC data base located on the web

Read ABIF formatted files

Read aligned sequence files in mase, clustal, phylip, fasta or msf format

read FASTA formatted files

Import GenMapper Bins configuration file

Import GenMapper Panels configuration file

Low level function to get the record count of the specified ACNUC index file

Low level function to read ACNUC SMJYT index files

Detection of replication-associated effects on base composition asymmetry in prokaryotic chromosomes.

Prediction of Coding DNA Sequences.

Total number of residues in an ACNUC list

Three aligned nucleic acid sequences

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

Ergheaf gur EBG-13 pvcurevat bs n fgevat

conversion of a string into a vector of chars

simple numerical encoding of a DNA sequence.

Save sequence names or accession numbers into a file

Biological Sequences Retrieval and Analysis

Sets the name of an ACNUC list identified by its rank

split a sequence into sub-sequences

Utility function to escape LaTeX special characters present in a string

Stutter ratio estimation

Exchange two R objects

Synonymous codons

Random synonymous coding sequence generation

to plot genetic code as in textbooks

Tests if regions located between Stop codons contain putative CDSs.

Tests if regions located between Stop codons contain putative CDSs.

A toy example of amino-acid counts in three proteins

A toy example of codon counts in three coding sequences

Translate nucleic acid sequences into proteins

Trim leading and/or trailing spaces in strings

Codon usage indices

Weight of each synonymous codon

Light absorption by the water column

Scans databases for a given sequence accession number

To get all words from an alphabet.

Positions of possibly degenerated motifs within sequences

Write sequence(s) into a file in fasta format

Statistical over- and under- representation of dinucleotides in a sequence