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seqinr (version 4.2-30)

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

4.2-30

License

GPL (>= 2)

Maintainer

Simon Penel

Last Published

April 5th, 2023

Functions in seqinr (4.2-30)

Expected numeric results for Ka and Ks computation

Forensic Genetic Profile Allelic Ladder Raw Data

utility data for seqinr

To Get Some Protein Statistics

Forensic Genetic Profile Raw Data

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

Sequence coming from a remote ACNUC data base

Vectors of coefficients to compute linear forms.

AA sequence in Fasta Format

Class for DNA sequence in Fasta Format

Class for sub-sequences

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

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

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

Computing an IUPAC nucleotide symbol

Estimation of baseline value

Constructor for class alignment

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

as.matrix.alignment

as.matrix.alignment

conversion of a vector of chars into a string

Returns a socket to the last opened database

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

Expansion of IUPAC nucleotide symbols

complements a nucleic acid sequence

Codon Adaptation Index (CAI) w tables

Base composition in ssDNA for 7 bacterial DNA

Codon Adaptation Index

To use a standard color with an alpha transparency chanel

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

To close a remote ACNUC database

Example of results obtained after a call to read.alignment

Number of subsequences in an ACNUC list

open and close a remote access to an ACNUC database

Cleveland plot for codon usage tables

Composition of dimer/trimer/etc oligomers

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

Graphical representation for nucleotide skews in prokaryotic chromosomes.

999 coding sequences from E. coli

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

To Compute the Theoretical Isoelectric Point

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

Fast Allele in Common Count

dia.bactgensize

Distribution of bacterial genome size from GOLD

Conversion of GenBank file into fasta file

Example of results obtained after a call to read.alignment

Mean zscore on 242 complete bacterial chromosomes

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

Consensus and profiles for sequence alignments

Generic function to get the length of sequences

Generic Function to get sequence annotations

Get the exponential growth of nucleic acid database content

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

To get the rank of a list from its name

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

Asks for information about an ACNUC list of specified rank

Generic function to extract sequence fragments

Generic function to get keywords associated to sequences

GC content and aerobiosis in bacteria

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

GC content and temperature in bacteria

Get help from an ACNUC server

Dot Plot Comparison of two sequences

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

crelistfromclientdata

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

To get available subsequence types in an opened ACNUC database

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

Generic function to translate coding sequences into proteins

Expected numeric results for Ka and Ks in extreme cases

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Description of databases known by an ACNUC server

Rename an R object

Extraction of Peak locations, Heights and Surfaces from ABIF data

Graphical representation of a recstat analysis.

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

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

GS500LIZ size standards

Identifiler allele names

Sequence permutation according to several different models

Electrophoregram plot for ABIF data

Prediction of origin and terminus of replication in bacteria.

Representation of Amplicon Size Ranges of a STR kit.

Generic function to get sequence data

Generic function to get the names of sequences

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

Simple plot of an allelic ladder from ABIF data

Example of results obtained after a call to read.alignment

Protein Molecular Weight

Fragment of the E. coli chromosome

To see what's inside the package seqinr

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

Utility function to parse answers from an ACNUC server

read FASTA formatted files

Select annotation lines in an ACNUC database

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

Zscore on three strains of Prochlorococcus marinus

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

Biological Sequences Retrieval and Analysis

Import GenMapper Panels configuration file

Three aligned nucleic acid sequences

Example of results obtained after a call to read.alignment

Example of results obtained after a call to read.alignment

Text representation of a sequence from an ACNUC server

Modification of an ACNUC list

Read ABIF formatted files

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

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

Import GenMapper Bins configuration file

split a sequence into sub-sequences

Total number of residues in an ACNUC list

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Ergheaf gur EBG-13 pvcurevat bs n fgevat

Prediction of Coding DNA Sequences.

Utility function to escape LaTeX special characters present in a string

Print method for objects from class qaw

Sets the name of an ACNUC list identified by its rank

test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.

conversion of a string into a vector of chars

to plot genetic code as in textbooks

Stutter ratio estimation

test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

Save sequence names or accession numbers into a file

rearranged.oriloc

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

simple numerical encoding of a DNA sequence.

A toy example of amino-acid counts in three proteins

Trim leading and/or trailing spaces in strings

Low level function to read ACNUC SMJYT index files

Positions of possibly degenerated motifs within sequences

Exchange two R objects

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

Codon usage indices

Write sequence(s) into a file in fasta format

where.is.this.acc

Scans databases for a given sequence accession number

Synonymous codons

Light absorption by the water column

A toy example of codon counts in three coding sequences

Weight of each synonymous codon

Random synonymous coding sequence generation

Translate nucleic acid sequences into proteins

To get all words from an alphabet.