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seqinr (version 4.2-36)

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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Install

install.packages('seqinr')

Monthly Downloads

17,087

Version

4.2-36

License

GPL (>= 2)

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Pull Requests

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Repository

https://github.com/lbbe-software/seqinr

Homepage

https://seqinr.r-forge.r-project.org/

Maintainer

Last Published

December 8th, 2023

Functions in seqinr (4.2-36)

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

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

Constructor for class alignment

Sequence coming from a remote ACNUC data base

Computing an IUPAC nucleotide symbol

Estimation of baseline value

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

Expansion of IUPAC nucleotide symbols

Codon Adaptation Index (CAI) w tables

To Compute the Theoretical Isoelectric Point

Consensus and profiles for sequence alignments

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

Composition of dimer/trimer/etc oligomers

Base composition in ssDNA for 7 bacterial DNA

as.matrix.alignment

as.matrix.alignment

open and close a remote access to an ACNUC database

conversion of a vector of chars into a string

Codon Adaptation Index

To close a remote ACNUC database

Class for DNA sequence in Fasta Format

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

Returns a socket to the last opened database

AA sequence in Fasta Format

Class for sub-sequences

Cleveland plot for codon usage tables

To use a standard color with an alpha transparency chanel

complements a nucleic acid sequence

Example of results obtained after a call to read.alignment

Graphical representation for nucleotide skews in prokaryotic chromosomes.

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

999 coding sequences from E. coli

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Graphical representation of a recstat analysis.

GC content and aerobiosis in bacteria

GC content and temperature in bacteria

Get the exponential growth of nucleic acid database content

To get available subsequence types in an opened ACNUC database

To get the rank of a list from its name

Generic Function to get sequence annotations

Generic function to translate coding sequences into proteins

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

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

Fast Allele in Common Count

Conversion of GenBank file into fasta file

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

Asks for information about an ACNUC list of specified rank

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

Sequence permutation according to several different models

Extraction of Peak locations, Heights and Surfaces from ABIF data

Number of subsequences in an ACNUC list

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

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

Generic function to get the length of sequences

To see what's inside the package seqinr

Fragment of the E. coli chromosome

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

Generic function to get keywords associated to sequences

Generic function to extract sequence fragments

Get help from an ACNUC server

crelistfromclientdata

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

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

Utility function to parse answers from an ACNUC server

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

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

Prediction of origin and terminus of replication in bacteria.

Mean zscore on 242 complete bacterial chromosomes

dia.bactgensize

Distribution of bacterial genome size from GOLD

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

Example of results obtained after a call to read.alignment

rearranged.oriloc

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

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Low level function to read ACNUC SMJYT index files

GS500LIZ size standards

Example of results obtained after a call to read.alignment

Identifiler allele names

Dot Plot Comparison of two sequences

Example of results obtained after a call to read.alignment

Modification of an ACNUC list

Representation of Amplicon Size Ranges of a STR kit.

Electrophoregram plot for ABIF data

Select annotation lines in an ACNUC database

Import GenMapper Bins configuration file

Generic function to get sequence data

read FASTA formatted files

Read ABIF formatted files

Generic function to get the names of sequences

Text representation of a sequence from an ACNUC server

Expected numeric results for Ka and Ks in extreme cases

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

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

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

Import GenMapper Panels configuration file

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

Three aligned nucleic acid sequences

Description of databases known by an ACNUC server

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

Rename an R object

Stutter ratio estimation

Prediction of Coding DNA Sequences.

Exchange two R objects

Random synonymous coding sequence generation

Synonymous codons

Total number of residues in an ACNUC list

simple numerical encoding of a DNA sequence.

Example of results obtained after a call to read.alignment

Save sequence names or accession numbers into a file

Simple plot of an allelic ladder from ABIF data

Protein Molecular Weight

where.is.this.acc

Scans databases for a given sequence accession number

To get all words from an alphabet.

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

to plot genetic code as in textbooks

A toy example of codon counts in three coding sequences

test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.

Ergheaf gur EBG-13 pvcurevat bs n fgevat

Print method for objects from class qaw

Zscore on three strains of Prochlorococcus marinus

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

conversion of a string into a vector of chars

Biological Sequences Retrieval and Analysis

Sets the name of an ACNUC list identified by its rank

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

Translate nucleic acid sequences into proteins

Weight of each synonymous codon

A toy example of amino-acid counts in three proteins

Write sequence(s) into a file in fasta format

Trim leading and/or trailing spaces in strings

Codon usage indices

test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.

Light absorption by the water column

split a sequence into sub-sequences

Positions of possibly degenerated motifs within sequences

Utility function to escape LaTeX special characters present in a string

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

Forensic Genetic Profile Allelic Ladder Raw Data

utility data for seqinr

To Get Some Protein Statistics