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seqinr (version 4.2-16)

Biological Sequences Retrieval and Analysis

Description

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 .

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Version

Install

install.packages('seqinr')

Monthly Downloads

19,759

Version

4.2-16

License

GPL (>= 2)

Maintainer

Simon Penel

Last Published

May 19th, 2022

Functions in seqinr (4.2-16)

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

as.matrix.alignment

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

crelistfromclientdata

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

dia.bactgensize

Distribution of bacterial genome size from GOLD

Number of subsequences in an ACNUC list

Mean zscore on 242 complete bacterial chromosomes

draw.rearranged.oriloc

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

rearranged.oriloc

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

plot.SeqAcnucWeb

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

extract.breakpoints

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

test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.

print.SeqAcnucWeb

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

where.is.this.acc

Scans databases for a given sequence accession number

To get all words from an alphabet.

test.co.recstat

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