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seqinr (version 4.2-8)

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

14,712

Version

4.2-8

License

GPL (>= 2)

Maintainer

Simon Penel

Last Published

June 9th, 2021

Functions in seqinr (4.2-8)

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

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

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

crelistfromclientdata

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

dia.bactgensize

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

draw.rearranged.oriloc

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.SeqAcnucWeb

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

extract.breakpoints

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

rearranged.oriloc

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

test.li.recstat

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

plot.SeqAcnucWeb

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

test.co.recstat

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

where.is.this.acc

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