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seqinr (version 1.0-5)

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 management under the ACNUC system.

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Version

Install

install.packages('seqinr')

Monthly Downloads

18,945

Version

1.0-5

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 (1.0-5)

Vectors of coefficients to compute linear forms.

Class for sub-sequences

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

Protein Molecular Weight

To Compute the Theoretical Isoelectric Point

Cleveland plot for codon usage tables

complements a nucleic acid sequence

read FASTA formatted files

conversion of a vector of chars into a string

Dot Plot Comparison of two sequences

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

Prediction of origin and terminus of replication in bacteria

split a sequence into sub-sequences

conversion of GenBank file into fasta file

Bacterial complete genome data from ncbi ftp site

Composition of dimer/trimer/etc nucleotides

A toy example of amino-acid counts in three proteins

To close a remote ACNUC database

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

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

conversion of a string into a vector of chars

Calculates the fractional G+C content of nucleic acid sequences

Class for DNA sequence in Fasta Format

Sequence coming from an ACNUC data bases located on the web

AA sequence in Fasta Format

GetFromSequence

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

dia.bactgensize

Distribution of bacterial genome size from GOLD

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

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

Weight of each synonymous codon

simple numerical encoding of a DNA sequence.

Random synonymous coding sequence generation

Sequence permutation according to several different models

A toy example of codon counts in three coding sequences

Codon usage indices

999 coding sequences from E. coli

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Synonymous codons

To Get Sequence Type

Expected numeric results for Ka and Ks computation

To Get Some Protein Statistics

crelistfromclientdata

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

Positions of possibly degenerated motifs within sequences

To see what's inside the package seqinr

Translate nucleic acid sequences

Biological Sequences Retrieval and Analysis

utility data for seqinr

Mean zscore on 242 complete bacterial chromosomes

Base composition in ssDNA for 7 bacterial DNA

Get the exponential growth of nucleic acid database content

to plot genetic code as in textbooks

To get all words from an alphabet.

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

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

to Get an Estimation of Ka and Ks

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

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Zscore on three strains of Prochlorococcus marinus

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

Write file in fasta format