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seqinr (version 4.2-5)

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

17,943

Version

4.2-5

License

GPL (>= 2)

Maintainer

Last Published

December 17th, 2020

Functions in seqinr (4.2-5)

Forensic Genetic Profile Raw Data

Forensic Genetic Profile Allelic Ladder Raw Data

To Get Some Protein Statistics

utility data for seqinr

Sequence coming from a remote ACNUC data base

Class for DNA sequence in Fasta Format

AA sequence in Fasta Format

Vectors of coefficients to compute linear forms.

Expected numeric results for Ka and Ks computation

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

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

Constructor for class alignment

Expansion of IUPAC nucleotide symbols

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

open and close a remote access to an ACNUC database

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

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

Computing an IUPAC nucleotide symbol

Estimation of baseline value

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

Codon Adaptation Index

Class for sub-sequences

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

conversion of a vector of chars into a string

Consensus and profiles for sequence alignments

To Compute the Theoretical Isoelectric Point

To use a standard color with an alpha transparency chanel

Codon Adaptation Index (CAI) w tables

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Graphical representation of a recstat analysis.

999 coding sequences from E. coli

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

Composition of dimer/trimer/etc oligomers

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

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

Base composition in ssDNA for 7 bacterial DNA

Number of subsequences in an ACNUC list

complements a nucleic acid sequence

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

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

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

To get available subsequence types in an opened ACNUC database

To close a remote ACNUC database

Generic function to get keywords associated to sequences

Get the exponential growth of nucleic acid database content

Example of results obtained after a call to read.alignment

Generic function to get the length of sequences

Bacterial complete genome data from ncbi ftp site

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

Asks for information about an ACNUC list of specified rank

Dot Plot Comparison of two sequences

Example of results obtained after a call to read.alignment

crelistfromclientdata

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

To get the rank of a list from its name

dia.bactgensize

Distribution of bacterial genome size from GOLD

GC content and temperature in bacteria

GC content and aerobiosis in bacteria

Extraction of Peak locations, Heights and Surfaces from ABIF data

Utility function to parse answers from an ACNUC server

Text representation of a sequence from an ACNUC server

Cleveland plot for codon usage tables

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

Graphical representation for nucleotide skews in prokaryotic chromosomes.

Fast Allele in Common Count

Import GenMapper Bins configuration file

Mean zscore on 242 complete bacterial chromosomes

Generic function to extract sequence fragments

Conversion of GenBank file into fasta file

Generic Function to get sequence annotations

Generic function to get sequence data

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

Import GenMapper Panels configuration file

Total number of residues in an ACNUC list

Three aligned nucleic acid sequences

Rename an R object

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

Expected numeric results for Ka and Ks in extreme cases

Read ABIF formatted files

Simple plot of an allelic ladder from ABIF data

Electrophoregram plot for ABIF data

Generic function to translate coding sequences into proteins

Modification of an ACNUC list

Translate nucleic acid sequences into proteins

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

Sets the name of an ACNUC list identified by its rank

Light absorption by the water column

split a sequence into sub-sequences

Identifiler allele names

where.is.this.acc

Scans databases for a given sequence accession number

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

Fragment of the E. coli chromosome

Prediction of origin and terminus of replication in bacteria.

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

Trim leading and/or trailing spaces in strings

Example of results obtained after a call to read.alignment

GS500LIZ size standards

Example of results obtained after a call to read.alignment

Get help from an ACNUC server

Representation of Amplicon Size Ranges of a STR kit.

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Sequence permutation according to several different models

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

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

simple numerical encoding of a DNA sequence.

Low level function to read ACNUC SMJYT index files

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

conversion of a string into a vector of chars

Random synonymous coding sequence generation

to plot genetic code as in textbooks

Example of results obtained after a call to read.alignment

Generic function to get the names of sequences

Save sequence names or accession numbers into a file

Biological Sequences Retrieval and Analysis

Protein Molecular Weight

Select annotation lines in an ACNUC database

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

test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.

To see what's inside the package seqinr

Description of databases known by an ACNUC server

test.li.recstat

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

read FASTA formatted files

Print method for objects from class qaw

Zscore on three strains of Prochlorococcus marinus

rearranged.oriloc

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

Prediction of Coding DNA Sequences.

Utility function to escape LaTeX special characters present in a string

Stutter ratio estimation

Codon usage indices

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

Weight of each synonymous codon

To get all words from an alphabet.

Exchange two R objects

Positions of possibly degenerated motifs within sequences

Synonymous codons

Ergheaf gur EBG-13 pvcurevat bs n fgevat

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

Write sequence(s) into a file in fasta format