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seqinr (version 3.6-1)

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

3.6-1

License

GPL (>= 2)

Maintainer

Simon Penel

Last Published

September 7th, 2019

Functions in seqinr (3.6-1)

Expected numeric results for Ka and Ks computation

Forensic Genetic Profile Allelic Ladder Raw Data

Class for DNA sequence in Fasta Format

Forensic Genetic Profile Raw Data

To Get Some Protein Statistics

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

utility data for seqinr

AA sequence in Fasta Format

Vectors of coefficients to compute linear forms.

Sequence coming from a remote ACNUC data base

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

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

Class for sub-sequences

Expansion of IUPAC nucleotide symbols

Constructor for class alignment

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

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

open and close a remote access to an ACNUC database

Estimation of baseline value

as.matrix.alignment

as.matrix.alignment

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

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

Codon Adaptation Index (CAI) w tables

conversion of a vector of chars into a string

Computing an IUPAC nucleotide symbol

Returns a socket to the last opened database

To Compute the Theoretical Isoelectric Point

Base composition in ssDNA for 7 bacterial DNA

Composition of dimer/trimer/etc oligomers

dia.bactgensize

Distribution of bacterial genome size from GOLD

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

Mean zscore on 242 complete bacterial chromosomes

complements a nucleic acid sequence

To use a standard color with an alpha transparency chanel

Cleveland plot for codon usage tables

999 coding sequences from E. coli

Number of subsequences in an ACNUC list

crelistfromclientdata

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

Graphical representation for nucleotide skews in prokaryotic chromosomes.

Get the exponential growth of nucleic acid database content

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Consensus and profiles for sequence alignments

Generic function to get the names of sequences

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

Conversion of GenBank file into fasta file

Fast Allele in Common Count

Graphical representation of a recstat analysis.

Generic function to get keywords associated to sequences

Generic function to get the length of sequences

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Codon Adaptation Index

Dot Plot Comparison of two sequences

GC content and temperature in bacteria

GC content and aerobiosis in bacteria

Asks for information about an ACNUC list of specified rank

To close a remote ACNUC database

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

Example of results obtained after a call to read.alignment

Fragment of the E. coli chromosome

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

Get help from an ACNUC server

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

Simple plot of an allelic ladder from ABIF data

Electrophoregram plot for ABIF data

GS500LIZ size standards

Bacterial complete genome data from ncbi ftp site

Text representation of a sequence from an ACNUC server

Rename an R object

Modification of an ACNUC list

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

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

Generic function to extract sequence fragments

Identifiler allele names

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

Prediction of origin and terminus of replication in bacteria.

Generic Function to get sequence annotations

Example of results obtained after a call to read.alignment

Example of results obtained after a call to read.alignment

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

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

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

Representation of Amplicon Size Ranges of a STR kit.

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Generic function to get sequence data

Import GenMapper Panels configuration file

Import GenMapper Bins configuration file

Generic function to translate coding sequences into proteins

Sequence permutation according to several different models

Save sequence names or accession numbers into a file

Biological Sequences Retrieval and Analysis

read FASTA formatted files

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

Read ABIF formatted files

rearranged.oriloc

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

Expected numeric results for Ka and Ks in extreme cases

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

Example of results obtained after a call to read.alignment

Low level function to read ACNUC SMJYT index files

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

To get available subsequence types in an opened ACNUC database

To get the rank of a list from its name

Prediction of Coding DNA Sequences.

test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.

test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.

Total number of residues in an ACNUC list

Three aligned nucleic acid sequences

Sets the name of an ACNUC list identified by its rank

simple numerical encoding of a DNA sequence.

conversion of a string into a vector of chars

Random synonymous coding sequence generation

Description of databases known by an ACNUC server

split a sequence into sub-sequences

Light absorption by the water column

A toy example of codon counts in three coding sequences

A toy example of amino-acid counts in three proteins

Exchange two R objects

Synonymous codons

Weight of each synonymous codon

Codon usage indices

where.is.this.acc

Scans databases for a given sequence accession number

Translate nucleic acid sequences into proteins

to plot genetic code as in textbooks

Trim leading and/or trailing spaces in strings

Utility function to parse answers from an ACNUC server

To see what's inside the package seqinr

Write sequence(s) into a file in fasta format

Protein Molecular Weight

Print method for objects from class qaw

Extraction of Peak locations, Heights and Surfaces from ABIF data

Zscore on three strains of Prochlorococcus marinus

Select annotation lines in an ACNUC database

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

Ergheaf gur EBG-13 pvcurevat bs n fgevat

Utility function to escape LaTeX special characters present in a string

Stutter ratio estimation

To get all words from an alphabet.

Positions of possibly degenerated motifs within sequences

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