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seqinr (version 1.0-3)

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

19,283

Version

1.0-3

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 (1.0-3)

Calculates the fractional GC2 content of nucleic acid sequences

Create codon usage table

Class for DNA sequence in Fasta Format

To close a remote ACNUC database

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

To Get Some Protein Statistics

dia.bactgensize

Distribution of bacterial genome size from GOLD

Cleveland plot for codon usage tables

Generic Function to obtain a fragment of a sequence

complement a nucleic sequence

Composition of dimer/trimer/etc nucleotides

AA sequence in Fasta Format

Positions of possibly degenerated motifs within sequences

Generic Function To Get a sequence

To see what's inside the package seqinr

conversion of GenBank file into fasta file

conversion of a vector of chars into a string

Generic Function To obtain the length of a sequence

999 coding sequences from E. coli

Get the exponential growth of nucleic acid database content

Vectors of coefficients to compute linear forms.

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

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

simple numerical encoding of a DNA sequence.

Class for sub-sequences

Read file in fasta format

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

conversion of a string into a vector of chars

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

Translate nucleic acid sequences

Prediction of origin and terminus of replication in bacteria

Calculates the fractional GC3 content of nucleic acid sequences

Generic Function To obtain the name of a sequence

to Get an Estimation of Ka and Ks

To get all words from an alphabet.

Bacterial complete genome data from ncbi ftp site

Read file in mase, clustal, phylip, fasta or msf format

To Get Sequence Type

utility data for seqinr

Generic Function to translate a sequence

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

to plot genetic code as in textbooks

Calculates the fractional GC content of nucleic acid sequences

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

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

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Base composition in ssDNA for 7 bacterial DNA

Generic Function to obtain annotation for a sequence

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

split a sequence into sub-sequences

To Compute the Theoretical Isoelectric Point

Sequence coming from an ACNUC data bases located on the web