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seqinr (version 1.0-6)

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

19,283

Version

1.0-6

License

GPL version 2 or newer

Maintainer

Simon Penel

Last Published

December 8th, 2023

Functions in seqinr (1.0-6)

getType

To Get Sequence Type
G+C Content

Calculates the fractional G+C content of nucleic acid sequences
AnoukResult

Expected numeric results for Ka and Ks computation
crelistfromclientdata

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

Codon usage indices
splitseq

split a sequence into sub-sequences
SeqFastadna

Class for DNA sequence in Fasta Format
computePI

To Compute the Theoretical Isoelectric Point
get.ncbi

Bacterial complete genome data from ncbi ftp site
plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence
s2n

simple numerical encoding of a DNA sequence.
SeqAcnucWeb

Sequence coming from an ACNUC data bases located on the web
oriloc

Prediction of origin and terminus of replication in bacteria
count

Composition of dimer/trimer/etc nucleotides
c2s

conversion of a vector of chars into a string
seqinr-package

Biological Sequences Retrieval and Analysis
dotPlot

Dot Plot Comparison of two sequences
ucoweight

Weight of each synonymous codon
EXP

Vectors of coefficients to compute linear forms.
dotchart.uco

Cleveland plot for codon usage tables
comp

complements a nucleic acid sequence
AAstat

To Get Some Protein Statistics
dist.alignment

Pairwise Distances from Aligned Protein or DNA/RNA Sequences
a

Converts amino-acid three-letter code into the one-letter one
get.db.growth

Get the exponential growth of nucleic acid database content
synsequence

Random synonymous coding sequence generation
read.fasta

read FASTA formatted files
aaa

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

AA sequence in Fasta Format
pmw

Protein Molecular Weight
gb2fasta

conversion of GenBank file into fasta file
aaindex

List of 544 physicochemical and biological properties for the 20 amino-acids
ec999

999 coding sequences from E. coli
SeqFrag

Class for sub-sequences
syncodons

Synonymous codons
s2c

conversion of a string into a vector of chars
choosebank

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

Write file in fasta format
tablecode

to plot genetic code as in textbooks
closebank

To close a remote ACNUC database
GetFromSequence

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

Zscore on three strains of Prochlorococcus marinus
dinucleotides

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

invers
words.pos

Positions of possibly degenerated motifs within sequences
kaks

to Get an Estimation of Ka and Ks
query

To get a list of sequence names from an ACNUC data base located on the web
gbk2g2

Conversion of a GenBank format file into a glimmer-like one
reverse.align

Reverse alignment - from protein sequence alignment to nucleic sequence alignment
toyaa

A toy example of amino-acid counts in three proteins
permutation

Sequence permutation according to several different models
n2s

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

Base composition in ssDNA for 7 bacterial DNA
toycodon

A toy example of codon counts in three coding sequences
read.alignment

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

Translate nucleic acid sequences
aacost

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

utility data for seqinr
dinucl

Mean zscore on 242 complete bacterial chromosomes
dia.bactgensize

Distribution of bacterial genome size from GOLD
words

To get all words from an alphabet.
lseqinr

To see what's inside the package seqinr