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seqinr (version 1.0-4)

Biological Sequences Retrieval and Analysis

Description

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data manadgment under the ACNUC system.

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Version

Install

install.packages('seqinr')

Monthly Downloads

19,759

Version

1.0-4

License

GPL version 2 or newer

Homepage

http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_home.php

Maintainer

Simon Penel

Last Published

December 8th, 2023

Functions in seqinr (1.0-4)

To Compute the Theoretical Isoelectric Point

conversion of GenBank file into fasta file

Composition of dimer/trimer/etc nucleotides

Generic Function To obtain the name of a sequence

Generic Function to obtain annotation for a sequence

conversion of a vector of chars into a string

Vectors of coefficients to compute linear forms.

Generic Function to get keyword(s) associated to a sequence

to Get an Estimation of Ka and Ks

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

Calculates the fractional G+C content of nucleic acid sequences

dia.bactgensize

Distribution of bacterial genome size from GOLD

Generic Function to translate a sequence

Weight of each synonymous codon

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

Zscore on three strains of Prochlorococcus marinus

Generic Function To obtain the length of a sequence

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

Generic Function To Get a sequence

Base composition in ssDNA for 7 bacterial DNA

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Get the exponential growth of nucleic acid database content

Sequence permutation according to several different models

Codon usage indices

Read file in fasta format

Generic Function to obtain a fragment of a sequence

utility data for seqinr

To see what's inside the package seqinr

To close a remote ACNUC database

To get all words from an alphabet.

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

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

To Get Some Protein Statistics

AA sequence in Fasta Format

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

Sequence coming from an ACNUC data bases located on the web

Bacterial complete genome data from ncbi ftp site

Expected numeric results for Ka and Ks computation

A toy example of amino-acid counts in three proteins

complement a nucleic sequence

Translate nucleic acid sequences

To Get Sequence Type

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

split a sequence into sub-sequences

Generic Function To obtain the Position of a Sequence on the Parent Sequence

Cleveland plot for codon usage tables

Random synonymous coding sequence generation

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

conversion of a string into a vector of chars

Class for DNA sequence in Fasta Format

Mean zscore on 242 complete bacterial chromosomes

Positions of possibly degenerated motifs within sequences

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

simple numerical encoding of a DNA sequence.

to plot genetic code as in textbooks

999 coding sequences from E. coli

A toy example of codon counts in three coding sequences

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Class for sub-sequences

Synonymous codons

Prediction of origin and terminus of replication in bacteria