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seqinr (version 3.4-5)

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

3.4-5

License

GPL (>= 2)

Maintainer

Last Published

August 1st, 2017

Functions in seqinr (3.4-5)

Forensic Genetic Profile Allelic Ladder Raw Data

Vectors of coefficients to compute linear forms.

To Get Some Protein Statistics

Expected numeric results for Ka and Ks computation

utility data for seqinr

Sequence coming from a remote ACNUC data base

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

Forensic Genetic Profile Raw Data

AA sequence in Fasta Format

Class for DNA sequence in Fasta Format

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

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

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

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

Codon Adaptation Index (CAI) w tables

Base composition in ssDNA for 7 bacterial DNA

Class for sub-sequences

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

as.matrix.alignment

as.matrix.alignment

Returns a socket to the last opened database

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

Composition of dimer/trimer/etc oligomers

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

Cleveland plot for codon usage tables

Graphical representation for nucleotide skews in prokaryotic chromosomes.

Get the exponential growth of nucleic acid database content

Bacterial complete genome data from ncbi ftp site

Generic function to get keywords associated to sequences

Generic function to get the length of sequences

Identifiler allele names

Computing an IUPAC nucleotide symbol

To Compute the Theoretical Isoelectric Point

Consensus and profiles for sequence alignments

Expansion of IUPAC nucleotide symbols

Constructor for class alignment

conversion of a vector of chars into a string

Codon Adaptation Index

To close a remote ACNUC database

Example of results obtained after a call to read.alignment

dia.bactgensize

Distribution of bacterial genome size from GOLD

Mean zscore on 242 complete bacterial chromosomes

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

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.

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

Utility function to parse answers from an ACNUC server

Extraction of Peak locations, Heights and Surfaces from ABIF data

Text representation of a sequence from an ACNUC server

To use a standard color with an alpha transparency chanel

complements a nucleic acid sequence

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Dot Plot Comparison of two sequences

GC content and aerobiosis in bacteria

GC content and temperature in bacteria

To get available subsequence types in an opened ACNUC database

To get the rank of a list from its name

Description of databases known by an ACNUC server

To see what's inside the package seqinr

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

Sequence permutation according to several different models

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

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 origin and terminus of replication in bacteria.

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

Generic Function to get sequence annotations

Generic function to extract sequence fragments

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

Generic function to get the names of sequences

Get help from an ACNUC server

GS500LIZ size standards

Modification of an ACNUC list

Rename an R object

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Representation of Amplicon Size Ranges of a STR kit.

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

Asks for information about an ACNUC list of specified rank

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

Fragment of the E. coli chromosome

Prediction of Coding DNA Sequences.

Random synonymous coding sequence generation

to plot genetic code as in textbooks

Codon usage indices

Low level function to read ACNUC SMJYT index files

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

Ergheaf gur EBG-13 pvcurevat bs n fgevat

Example of results obtained after a call to read.alignment

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

read FASTA formatted files

Save sequence names or accession numbers into a file

Weight of each synonymous codon

Number of subsequences in an ACNUC list

crelistfromclientdata

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

999 coding sequences from E. coli

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

Fast Allele in Common Count

Biological Sequences Retrieval and Analysis

Utility function to escape LaTeX special characters present in a string

Stutter ratio estimation

Light absorption by the water column

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.

To get all words from an alphabet.

Positions of possibly degenerated motifs within sequences

Example of results obtained after a call to read.alignment

Electrophoregram plot for ABIF data

Simple plot of an allelic ladder from ABIF data

Import GenMapper Bins configuration file

Import GenMapper Panels configuration file

conversion of a string into a vector of chars

simple numerical encoding of a DNA sequence.

Exchange two R objects

where.is.this.acc

Scans databases for a given sequence accession number

Conversion of GenBank file into fasta file

Generic function to get sequence data

Generic function to translate coding sequences into proteins

Expected numeric results for Ka and Ks in extreme cases

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

Example of results obtained after a call to read.alignment

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

Protein Molecular Weight

Select annotation lines in an ACNUC database

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

Read ABIF formatted files

Total number of residues in an ACNUC list

Three aligned nucleic acid sequences

Sets the name of an ACNUC list identified by its rank

split a sequence into sub-sequences

Translate nucleic acid sequences into proteins

Trim leading and/or trailing spaces in strings

Synonymous codons

A toy example of amino-acid counts in three proteins

A toy example of codon counts in three coding sequences

Write sequence(s) into a file in fasta format

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