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seqinr (version 1.0-1)

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

1.0-1

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 (1.0-1)

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Generic Function to obtain annotation for a sequence

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

Vectors of coefficients to compute linear forms.

conversion of a vector of chars into a string

To see what's inside the package seqinr

Class for DNA sequence in Fasta Format

Get the exponential growth of nucleic acid database content

Sequence coming from an ACNUC data bases located on the web

to Get an Estimation of Ka and Ks

To Compute the Theoretical Isoelectric Point

Calculates the fractional GC2 content of nucleic acid sequences

simple numerical encoding of a DNA sequence.

Class for sub-sequences

To Get Some Protein Statistics

dia.bactgensize

Distribution of bacterial genome size from GOLD

Composition of dimer/trimer/etc nucleotides

Calculates the fractional GC3 content of nucleic acid sequences

AA sequence in Fasta Format

to plot genetic code as in textbooks

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

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

Prediction of origin and terminus of replication in bacteria

999 coding sequences from E. coli

Read file in fasta format

conversion of GenBank file into fasta file

Generic Function to translate a sequence

Generic Function To obtain the length of a sequence

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

To Get Sequence Type

Create codon usage table

Positions of possibly degenerated motifs within sequences

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Generic Function To Get a sequence

Translate nucleic acid sequences

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

Cleveland plot for codon usage tables

To get all words from an alphabet.

Base composition in ssDNA for 7 bacterial DNA

Generic Function To obtain the name of a sequence

split a sequence into sub-sequences

utility data for seqinr

complement a nucleic sequence

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

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

conversion of a string into a vector of chars

Bacterial complete genome data from ncbi ftp site

Calculates the fractional GC content of nucleic acid sequences

Generic Function to obtain a fragment of a sequence

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

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

To close a remote ACNUC database

Mean zscore on 242 complete bacterial chromosomes

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

Dot Plot Comparison of two sequences

Expected numeric results for Ka and Ks computation

Zscore on three strains of Prochlorococcus marinus

Random synonymous coding sequence generation

GetFromSequence

Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence

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

Sequence permutation according to several different models

Weight of each synonymous codon

Calculates the fractional G+C content of nucleic acid sequences

Protein Molecular Weight

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

A toy example of amino-acid counts in three proteins

A toy example of codon counts in three coding sequences

crelistfromclientdata

To create on server a bitlist from data lines sent by client

Synonymous codons

Write file in fasta format

Biological Sequences Retrieval and Analysis

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