Package: seqinr 4.2-44

Simon Penel

seqinr: Biological Sequences Retrieval and Analysis

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 <doi:10.1093/nar/12.1Part1.121>.

Authors:Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

seqinr_4.2-44.tar.gz
seqinr_4.2-44.zip(r-4.7)seqinr_4.2-44.zip(r-4.6)seqinr_4.2-44.zip(r-4.5)
seqinr_4.2-44.tgz(r-4.6-x86_64)seqinr_4.2-44.tgz(r-4.6-arm64)seqinr_4.2-44.tgz(r-4.5-x86_64)seqinr_4.2-44.tgz(r-4.5-arm64)
seqinr_4.2-44.tar.gz(r-4.7-arm64)seqinr_4.2-44.tar.gz(r-4.7-x86_64)seqinr_4.2-44.tar.gz(r-4.6-arm64)seqinr_4.2-44.tar.gz(r-4.6-x86_64)
seqinr_4.2-44.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
seqinr/json (API)
NEWS

# Install 'seqinr' in R:

install.packages('seqinr', repos = c('https://lbbe-software.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lbbe-software/seqinr/issues

Uses libs:

zlib– Compression library

Datasets:

aacost - Aerobic cost of amino-acids in Escherichia coli and G+C classes
aaindex - List of 544 physicochemical and biological properties for the 20 amino-acids
AnoukResult - Expected numeric results for Ka and Ks computation
caitab - Codon Adaptation Index (CAI) w tables
chargaff - Base composition in ssDNA for 7 bacterial DNA
clustal - Example of results obtained after a call to read.alignment
dinucl - Mean zscore on 242 complete bacterial chromosomes
ec999 - 999 coding sequences from E. coli
ECH - Forensic Genetic Profile Allelic Ladder Raw Data
EXP - Vectors of coefficients to compute linear forms.
fasta - Example of results obtained after a call to read.alignment
gcO2 - GC content and aerobiosis in bacteria
gcT - GC content and temperature in bacteria
gs500liz - GS500LIZ size standards
identifiler - Identifiler allele names
JLO - Forensic Genetic Profile Raw Data
kaksTorture - Expected numeric results for Ka and Ks in extreme cases
m16j - Fragment of the E. coli chromosome
mase - Example of results obtained after a call to read.alignment
msf - Example of results obtained after a call to read.alignment
phylip - Example of results obtained after a call to read.alignment
pK - PK values for the side chain of charged amino acids from various sources
prochlo - Zscore on three strains of Prochlorococcus marinus
revaligntest - Three aligned nucleic acid sequences
SEQINR.UTIL - Utility data for seqinr
SEQINR.UTIL - Utility data for seqinr
toyaa - A toy example of amino-acid counts in three proteins
toycodon - A toy example of codon counts in three coding sequences
waterabs - Light absorption by the water column

On CRAN:

zlib

11.79 score 5 stars 128 packages 4.9k scripts 33k downloads 110 mentions 204 exports 9 dependencies

Last updated from:c84024d1dc. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	150
linux-devel-x86_64	OK	158
source / vignettes	OK	186
linux-release-arm64	OK	144
linux-release-x86_64	OK	141
macos-release-arm64	OK	102
macos-release-x86_64	OK	231
macos-oldrel-arm64	OK	135
macos-oldrel-x86_64	OK	191
windows-devel	OK	138
windows-release	OK	122
windows-oldrel	OK	120
wasm-release	OK	121

Exports:.seqinrEnv a aaa AAstat acnucclose acnucopen al2bp alllistranks alr amb as.alignment as.matrix.alignment as.SeqAcnucWeb as.SeqFastaAA as.SeqFastadna as.SeqFrag autosocket baselineabif bma c2s cai cfl choosebank circle clfcd clientid closebank col2alpha comp computePI con consensus count countfreelists countsubseqs crelistfromclientdata css dia.bactgensize dia.db.growth dist.alignment dotchart.uco dotPlot draw.oriloc draw.rearranged.oriloc draw.recstat exseq extract.breakpoints extractseqs fastacc gb2fasta gbk2g2 gbk2g2.euk GC GC1 GC2 GC3 GCpos get.db.growth getAnnot getAnnot.default getAnnot.list getAnnot.logical getAnnot.qaw getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA getAnnot.SeqFastadna getAttributsocket getFrag getFrag.character getFrag.default getFrag.list getFrag.logical getFrag.qaw getFrag.SeqAcnucWeb getFrag.SeqFastaAA getFrag.SeqFastadna getFrag.SeqFrag getKeyword getKeyword.default getKeyword.list getKeyword.logical getKeyword.qaw getKeyword.SeqAcnucWeb getLength getLength.character getLength.default getLength.list getLength.logical getLength.qaw getLength.SeqAcnucWeb getLength.SeqFastaAA getLength.SeqFastadna getLength.SeqFrag getlistrank getliststate getLocation getLocation.default getLocation.list getLocation.logical getLocation.qaw getLocation.SeqAcnucWeb getName getName.default getName.list getName.logical getName.qaw getName.SeqAcnucWeb getName.SeqFastaAA getName.SeqFastadna getName.SeqFrag getNumber.socket getSequence getSequence.character getSequence.default getSequence.list getSequence.logical getSequence.qaw getSequence.SeqAcnucWeb getSequence.SeqFastaAA getSequence.SeqFastadna getSequence.SeqFrag getTrans getTrans.character getTrans.default getTrans.list getTrans.logical getTrans.qaw getTrans.SeqAcnucWeb getTrans.SeqFastadna getTrans.SeqFrag getType gfrag ghelp gln glr gls is.SeqAcnucWeb is.SeqFastaAA is.SeqFastadna is.SeqFrag isenum isn kaks kdb knowndbs lseqinr modifylist move mv n2s oriloc parser.socket peakabif permutation pga plot.SeqAcnucWeb plotabif plotladder plotPanels pmw prepgetannots prettyseq print.qaw print.SeqAcnucWeb query quitacnuc read.abif read.alignment read.fasta readBins readfirstrec readPanels readsmj rearranged.oriloc recstat residuecount reverse.align rho rot13 s2c s2n savelist SEQINR.UTIL setlistname splitseq stresc stutterabif summary.SeqFastaAA summary.SeqFastadna swap syncodons synsequence tablecode test.co.recstat test.li.recstat translate trimSpace uco ucoweight where.is.this.acc words words.pos write.fasta zscore

Dependencies:ade4 lattice MASS nlme pixmap Rcpp RcppArmadillo segmented sp

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Biological Sequences Retrieval and Analysis	seqinr-package seqinr
Converts amino-acid three-letter code into the one-letter one	a
Converts amino-acid one-letter code into the three-letter one	aaa
Aerobic cost of amino-acids in Escherichia coli and G+C classes	aacost
List of 544 physicochemical and biological properties for the 20 amino-acids	aaindex
To Get Some Protein Statistics	AAstat
open and close a remote access to an ACNUC database	acnucclose acnucopen clientid quitacnuc
To Convert a forensic microsatellite allele name into its length in base pairs	al2bp
To get the count of existing lists and all their ranks on server	alllistranks alr
Expansion of IUPAC nucleotide symbols	amb
Expected numeric results for Ka and Ks computation	AnoukResult
Constructor for class alignment	as.alignment
as.matrix.alignment	as.matrix.alignment
Returns a socket to the last opened database	autosocket
Estimation of baseline value	baselineabif
Computing an IUPAC nucleotide symbol	bma
conversion of a vector of chars into a string	c2s
Codon Adaptation Index	cai
Codon Adaptation Index (CAI) w tables	caitab
Base composition in ssDNA for 7 bacterial DNA	chargaff
To select a database structured under ACNUC and located on the web	.seqinrEnv choosebank
Draws a circle	circle
To close a remote ACNUC database	closebank
Example of results obtained after a call to read.alignment	clustal
To use a standard color with an alpha transparency chanel	col2alpha
complements a nucleic acid sequence	comp
To Compute the Theoretical Isoelectric Point	computePI
Consensus and profiles for sequence alignments	con consensus
Composition of dimer/trimer/etc oligomers	count
The number of free lists available and annotation lines in an ACNUC server	cfl countfreelists
Number of subsequences in an ACNUC list	countsubseqs css
To create on server an ACNUC list from data lines sent by client	clfcd crelistfromclientdata
Distribution of bacterial genome size from GOLD	dia.bactgensize
Mean zscore on 242 complete bacterial chromosomes	dinucl
Statistical over- and under- representation of dinucleotides in a sequence	rho zscore
Pairwise Distances from Aligned Protein or DNA/RNA Sequences	dist.alignment
Cleveland plot for codon usage tables	dotchart.uco
Dot Plot Comparison of two sequences	dotPlot
Graphical representation for nucleotide skews in prokaryotic chromosomes.	draw.oriloc
Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.	draw.rearranged.oriloc
Graphical representation of a recstat analysis.	draw.recstat
999 coding sequences from E. coli	ec999
Forensic Genetic Profile Allelic Ladder Raw Data	ECH
Vectors of coefficients to compute linear forms.	EXP
Extraction of breakpoint positions on the rearranged nucleotide skews.	extract.breakpoints
To extract the sequences information of a sequence or a list of sequence in different formats	exseq extractseqs
Example of results obtained after a call to read.alignment	fasta
Fast Allele in Common Count	fastacc
Calculates the fractional G+C content of nucleic acid sequences.	GC GC1 GC2 GC3 GCpos
Conversion of GenBank file into fasta file	gb2fasta
Conversion of a GenBank format file into a glimmer-like one	gbk2g2
Conversion of a GenBank format file into a glimmer-like one. Eukaryotic version.	gbk2g2.euk
GC content and aerobiosis in bacteria	gcO2
GC content and temperature in bacteria	gcT
Get the exponential growth of nucleic acid database content	dia.db.growth get.db.growth
Generic Function to get sequence annotations	getAnnot getAnnot.default getAnnot.list getAnnot.logical getAnnot.qaw getAnnot.SeqAcnucWeb getAnnot.SeqFastaAA getAnnot.SeqFastadna readAnnots.socket
Generic function to extract sequence fragments	getFrag getFrag.character getFrag.default getFrag.list getFrag.logical getFrag.qaw getFrag.SeqAcnucWeb getFrag.SeqFastaAA getFrag.SeqFastadna getFrag.SeqFrag
Generic function to get keywords associated to sequences	getKeyword getKeyword.default getKeyword.list getKeyword.logical getKeyword.qaw getKeyword.SeqAcnucWeb
Generic function to get the length of sequences	getLength getLength.character getLength.default getLength.list getLength.logical getLength.qaw getLength.SeqAcnucWeb getLength.SeqFastaAA getLength.SeqFastadna getLength.SeqFrag
To get the rank of a list from its name	getlistrank glr
Asks for information about an ACNUC list of specified rank	getliststate gln gls
Generic function to get the location of subsequences on the parent sequence	getLocation getLocation.default getLocation.list getLocation.logical getLocation.qaw getLocation.SeqAcnucWeb
Generic function to get the names of sequences	getName getName.default getName.list getName.logical getName.qaw getName.SeqAcnucWeb getName.SeqFastaAA getName.SeqFastadna getName.SeqFrag
Generic function to get sequence data	getSequence getSequence.character getSequence.default getSequence.list getSequence.logical getSequence.qaw getSequence.SeqAcnucWeb getSequence.SeqFastaAA getSequence.SeqFastadna getSequence.SeqFrag
Generic function to translate coding sequences into proteins	getTrans getTrans.character getTrans.default getTrans.list getTrans.logical getTrans.qaw getTrans.SeqAcnucWeb getTrans.SeqFastadna getTrans.SeqFrag
To get available subsequence types in an opened ACNUC database	getType
Extract sequence identified by name or by number from an ACNUC server	gfrag
Get help from an ACNUC server	ghelp
GS500LIZ size standards	gs500liz
Identifiler allele names	identifiler
Get the ACNUC number of a sequence from its name or accession number	getAttributsocket getNumber.socket isenum isn
Forensic Genetic Profile Raw Data	JLO
Ka and Ks, also known as dn and ds, computation	kaks
Expected numeric results for Ka and Ks in extreme cases	kaksTorture
Description of databases known by an ACNUC server	kdb knowndbs
To see what's inside the package seqinr	lseqinr
Fragment of the E. coli chromosome	m16j
Example of results obtained after a call to read.alignment	mase
Modification of an ACNUC list	modifylist
Rename an R object	move mv
Example of results obtained after a call to read.alignment	msf
function to convert the numeric encoding of a DNA sequence into a vector of characters	n2s
Prediction of origin and terminus of replication in bacteria.	oriloc
Utility function to parse answers from an ACNUC server	parser.socket
Extraction of Peak locations, Heights and Surfaces from ABIF data	peakabif
Sequence permutation according to several different models	permutation
Example of results obtained after a call to read.alignment	phylip
pK values for the side chain of charged amino acids from various sources	pK
To Plot Subsequences on the Parent Sequence	plot.SeqAcnucWeb
Electrophoregram plot for ABIF data	plotabif
Simple plot of an allelic ladder from ABIF data	plotladder
Representation of Amplicon Size Ranges of a STR kit.	plotPanels
Protein Molecular Weight	pmw
Select annotation lines in an ACNUC database	pga prepgetannots
Text representation of a sequence from an ACNUC server	prettyseq
Print method for objects from class qaw	print.qaw
Print method for objects from class SeqAcnucWeb	print.SeqAcnucWeb
Zscore on three strains of Prochlorococcus marinus	prochlo
To get a list of sequence names from an ACNUC data base located on the web	query
Read ABIF formatted files	read.abif
Read aligned sequence files in mase, clustal, phylip, fasta or msf format	read.alignment
read FASTA formatted files	FASTA read.fasta readfasta
Import GenMapper Bins configuration file	readBins
Low level function to get the record count of the specified ACNUC index file	readfirstrec
Import GenMapper Panels configuration file	readPanels
Low level function to read ACNUC SMJYT index files	readsmj
Detection of replication-associated effects on base composition asymmetry in prokaryotic chromosomes.	rearranged.oriloc
Prediction of Coding DNA Sequences.	recstat
Total number of residues in an ACNUC list	residuecount
Three aligned nucleic acid sequences	revaligntest
Reverse alignment - from protein sequence alignment to nucleic sequence alignment	reverse.align
Ergheaf gur EBG-13 pvcurevat bs n fgevat	rot13
conversion of a string into a vector of chars	s2c
simple numerical encoding of a DNA sequence.	s2n
Save sequence names or accession numbers into a file	savelist
Sequence coming from a remote ACNUC data base	as.SeqAcnucWeb is.SeqAcnucWeb SeqAcnucWeb
AA sequence in Fasta Format	as.SeqFastaAA is.SeqFastaAA SeqFastaAA summary.SeqFastaAA
Class for DNA sequence in Fasta Format	as.SeqFastadna is.SeqFastadna SeqFastadna summary.SeqFastadna
Class for sub-sequences	as.SeqFrag is.SeqFrag SeqFrag
utility data for seqinr	SEQINR.UTIL
Sets the name of an ACNUC list identified by its rank	setlistname
split a sequence into sub-sequences	splitseq
Utility function to escape LaTeX special characters present in a string	stresc
Stutter ratio estimation	stutterabif
Exchange two R objects	swap
Synonymous codons	syncodons
Random synonymous coding sequence generation	synsequence
to plot genetic code as in textbooks	tablecode
Tests if regions located between Stop codons contain putative CDSs.	test.co.recstat
Tests if regions located between Stop codons contain putative CDSs.	test.li.recstat
A toy example of amino-acid counts in three proteins	toyaa
A toy example of codon counts in three coding sequences	toycodon
Translate nucleic acid sequences into proteins	translate
Trim leading and/or trailing spaces in strings	trimSpace
Codon usage indices	rscu uco
Weight of each synonymous codon	ucoweight
Light absorption by the water column	waterabs
Scans databases for a given sequence accession number	where.is.this.acc
To get all words from an alphabet.	words
Positions of possibly degenerated motifs within sequences	words.pos
Write sequence(s) into a file in fasta format	write.fasta