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seqinr (version 1.0-2)

seqinr

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

1.0-2

License

GPL version 2 or newer

Homepage

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

Maintainer

seqinr

Last Published

December 8th, 2023

Functions in seqinr (1.0-2)

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Sequence coming from an ACNUC data bases located on the web

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Composition of dimer/trimer/etc nucleotides

complement a nucleic sequence

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

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

To Get Sequence Type

Calculates the fractional GC2 content of nucleic acid sequences

AA sequence in Fasta Format

conversion of GenBank file into fasta file

Calculates the fractional GC content of nucleic acid sequences

To see what's inside the package seqinr

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

Cleveland plot for codon usage tables

Base composition in ssDNA for 7 bacterial DNA

Generic Function to obtain a fragment of a sequence

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

Class for sub-sequences

Generic Function to translate a sequence

To Get Some Protein Statistics

simple numerical encoding of a DNA sequence.

Calculates the fractional GC3 content of nucleic acid sequences

dia.bactgensize

Distribution of bacterial genome size from GOLD

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

conversion of a vector of chars into a string

Bacterial complete genome data from ncbi ftp site

Generic Function to obtain annotation for a sequence

Generic Function To obtain the name of a sequence

Get the exponential growth of nucleic acid database content

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

Vectors of coefficients to compute linear forms.

999 coding sequences from E. coli

conversion of a string into a vector of chars

utility data for seqinr

Class for DNA sequence in Fasta Format

To Compute the Theoretical Isoelectric Point

Prediction of origin and terminus of replication in bacteria

to Get an Estimation of Ka and Ks

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

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

Generic Function To Get a sequence

Read file in fasta format

Generic Function To obtain the length of a sequence

split a sequence into sub-sequences

To get all words from an alphabet.

to plot genetic code as in textbooks

Create codon usage table

Positions of possibly degenerated motifs within sequences

Translate nucleic acid sequences