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seqinr (version 4.2-23)

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

4.2-23

License

GPL (>= 2)

Maintainer

Simon Penel

Last Published

November 28th, 2022

Functions in seqinr (4.2-23)

AA sequence in Fasta Format

utility data for seqinr

Forensic Genetic Profile Allelic Ladder Raw Data

Forensic Genetic Profile Raw Data

To Get Some Protein Statistics

Vectors of coefficients to compute linear forms.

Expected numeric results for Ka and Ks computation

Class for DNA sequence in Fasta Format

Sequence coming from a remote ACNUC data base

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

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

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

Constructor for class alignment

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

Class for sub-sequences

open and close a remote access to an ACNUC database

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

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

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

Expansion of IUPAC nucleotide symbols

Codon Adaptation Index (CAI) w tables

as.matrix.alignment

as.matrix.alignment

Base composition in ssDNA for 7 bacterial DNA

Codon Adaptation Index

Returns a socket to the last opened database

conversion of a vector of chars into a string

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

Estimation of baseline value

Computing an IUPAC nucleotide symbol

Consensus and profiles for sequence alignments

Composition of dimer/trimer/etc oligomers

To close a remote ACNUC database

To Compute the Theoretical Isoelectric Point

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

complements a nucleic acid sequence

To use a standard color with an alpha transparency chanel

Example of results obtained after a call to read.alignment

Number of subsequences in an ACNUC list

crelistfromclientdata

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

Cleveland plot for codon usage tables

Dot Plot Comparison of two sequences

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Graphical representation of a recstat analysis.

Example of results obtained after a call to read.alignment

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

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

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

GC content and aerobiosis in bacteria

Mean zscore on 242 complete bacterial chromosomes

dia.bactgensize

Distribution of bacterial genome size from GOLD

GC content and temperature in bacteria

Get the exponential growth of nucleic acid database content

Fast Allele in Common Count

Generic function to extract sequence fragments

Generic Function to get sequence annotations

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

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

Conversion of GenBank file into fasta file

Generic function to get the length of sequences

Asks for information about an ACNUC list of specified rank

Graphical representation for nucleotide skews in prokaryotic chromosomes.

Generic function to get the names of sequences

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

999 coding sequences from E. coli

Expected numeric results for Ka and Ks in extreme cases

Generic function to get keywords associated to sequences

Prediction of origin and terminus of replication in bacteria.

Description of databases known by an ACNUC server

To get the rank of a list from its name

Generic function to translate coding sequences into proteins

Simple plot of an allelic ladder from ABIF data

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

Example of results obtained after a call to read.alignment

Modification of an ACNUC list

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

To see what's inside the package seqinr

Example of results obtained after a call to read.alignment

Generic function to get sequence data

Protein Molecular Weight

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

To get available subsequence types in an opened ACNUC database

Select annotation lines in an ACNUC database

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

Get help from an ACNUC server

Text representation of a sequence from an ACNUC server

Read ABIF formatted files

Identifiler allele names

GS500LIZ size standards

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

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

Extraction of Peak locations, Heights and Surfaces from ABIF data

Zscore on three strains of Prochlorococcus marinus

Fragment of the E. coli chromosome

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

Sequence permutation according to several different models

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

Three aligned nucleic acid sequences

read FASTA formatted files

Utility function to parse answers from an ACNUC server

Import GenMapper Bins configuration file

Biological Sequences Retrieval and Analysis

simple numerical encoding of a DNA sequence.

Save sequence names or accession numbers into a file

Electrophoregram plot for ABIF data

Import GenMapper Panels configuration file

Stutter ratio estimation

where.is.this.acc

Scans databases for a given sequence accession number

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

Synonymous codons

Random synonymous coding sequence generation

Print method for objects from class qaw

Representation of Amplicon Size Ranges of a STR kit.

Exchange two R objects

Positions of possibly degenerated motifs within sequences

Prediction of Coding DNA Sequences.

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

Ergheaf gur EBG-13 pvcurevat bs n fgevat

Low level function to read ACNUC SMJYT index files

Sets the name of an ACNUC list identified by its rank

to plot genetic code as in textbooks

To get all words from an alphabet.

conversion of a string into a vector of chars

test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.

Total number of residues in an ACNUC list

Translate nucleic acid sequences into proteins

Weight of each synonymous codon

A toy example of codon counts in three coding sequences

Write sequence(s) into a file in fasta format

rearranged.oriloc

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

test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.

Light absorption by the water column

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

A toy example of amino-acid counts in three proteins

split a sequence into sub-sequences

Trim leading and/or trailing spaces in strings

Utility function to escape LaTeX special characters present in a string

Codon usage indices