seqinr: Biological Sequences Retrieval and Analysis

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.

Install the latest version of this package by entering the following in R:
AuthorDelphine 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]
Date of publication2017-04-06 10:32:42 UTC
MaintainerSimon Penel <>
LicenseGPL (>= 2)

View on CRAN

Man pages

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

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

aacost: Aerobic cost of amino-acids in Escherichia coli and G+C...

aaindex: List of 544 physicochemical and biological properties for the...

AAstat: To Get Some Protein Statistics

acnucopen: open and close a remote access to an ACNUC database

al2bp: To Convert a forensic microsatellite allele name into its...

alllistranks: To get the count of existing lists and all their ranks on...

amb: Expansion of IUPAC nucleotide symbols

AnoukResult: Expected numeric results for Ka and Ks computation

as.alignment: Constructor for class alignment

as.matrix.alignment: as.matrix.alignment

autosocket: Returns a socket to the last opened database

baselineabif: Estimation of baseline value

bma: Computing an IUPAC nucleotide symbol

c2s: conversion of a vector of chars into a string

cai: Codon Adaptation Index

caitab: Codon Adaptation Index (CAI) w tables

chargaff: Base composition in ssDNA for 7 bacterial DNA

choosebank: To select a database structured under ACNUC and located on...

circle: Draws a circle

closebank: To close a remote ACNUC database

clustal: Example of results obtained after a call to read.alignment

col2alpha: To use a standard color with an alpha transparency chanel

comp: complements a nucleic acid sequence

computePI: To Compute the Theoretical Isoelectric Point

consensus: Consensus and profiles for sequence alignments

count: Composition of dimer/trimer/etc oligomers

countfreelists: The number of free lists available and annotation lines in an...

countsubseqs: Number of subsequences in an ACNUC list

crelistfromclientdata: To create on server an ACNUC list from data lines sent by...

dia.bactgensize: Distribution of bacterial genome size from GOLD

dinucl: Mean zscore on 242 complete bacterial chromosomes

dist.alignment: Pairwise Distances from Aligned Protein or DNA/RNA Sequences

dotchart.uco: Cleveland plot for codon usage tables

dotPlot: Dot Plot Comparison of two sequences

draw.oriloc: Graphical representation for nucleotide skews in prokaryotic...

draw.rearranged.oriloc: Graphical representation for rearranged nucleotide skews in...

draw.recstat: Graphical representation of a recstat analysis.

ec999: 999 coding sequences from E. coli

ECH: Forensic Genetic Profile Allelic Ladder Raw Data

EXP: Vectors of coefficients to compute linear forms.

extract.breakpoints: Extraction of breakpoint positions on the rearranged...

extractseqs: To extract the sequences information of a sequence or a list...

fasta: Example of results obtained after a call to read.alignment

fastacc: Fast Allele in Common Count

gb2fasta: Conversion of GenBank file into fasta file

gbk2g2: Conversion of a GenBank format file into a glimmer-like one

gbk2g2.euk: Conversion of a GenBank format file into a glimmer-like one....

GC: Calculates the fractional G+C content of nucleic acid...

gcO2: GC content and aerobiosis in bacteria

gcT: GC content and temperature in bacteria

getAnnot: Generic Function to get sequence annotations

get.db.growth: Get the exponential growth of nucleic acid database content

getFrag: Generic function to extract sequence fragments

getKeyword: Generic function to get keywords associated to sequences

getLength: Generic function to get the length of sequences

getlistrank: To get the rank of a list from its name

getliststate: Asks for information about an ACNUC list of specified rank

getLocation: Generic function to get the location of subsequences on the...

getName: Generic function to get the names of sequences

get.ncbi: Bacterial complete genome data from ncbi ftp site

getSequence: Generic function to get sequence data

getTrans: Generic function to translate coding sequences into proteins

getType: To get available subsequence types in an opened ACNUC...

gfrag: Extract sequence identified by name or by number from an...

ghelp: Get help from an ACNUC server

gs500liz: GS500LIZ size standards

identifiler: Identifiler allele names

isenum: Get the ACNUC number of a sequence from its name or accession...

JLO: Forensic Genetic Profile Raw Data

kaks: Ka and Ks, also known as dn and ds, computation

knowndbs: Description of databases known by an ACNUC server

lseqinr: To see what's inside the package seqinr

m16j: Fragment of the E. coli chromosome

mase: Example of results obtained after a call to read.alignment

modifylist: Modification of an ACNUC list

move: Rename an R object

msf: Example of results obtained after a call to read.alignment

n2s: function to convert the numeric encoding of a DNA sequence...

oriloc: Prediction of origin and terminus of replication in bacteria.

parser.socket: Utility function to parse answers from an ACNUC server

peakabif: Extraction of Peak locations, Heights and Surfaces from ABIF...

permutation: Sequence permutation according to several different models

phylip: Example of results obtained after a call to read.alignment

pK: pK values for the side chain of charged amino acids from...

plotabif: Electrophoregram plot for ABIF data

plotladder: Simple plot of an allelic ladder from ABIF data

plotPanels: Representation of Amplicon Size Ranges of a STR kit.

plot.SeqAcnucWeb: To Plot Subsequences on the Parent Sequence

pmw: Protein Molecular Weight

prepgatannots: Select annotation lines in an ACNUC database

prettyseq: Text representation of a sequence from an ACNUC server

print.qaw: Print method for objects from class qaw

print.SeqAcnucWeb: Print method for objects from class SeqAcnucWeb

prochlo: Zscore on three strains of Prochlorococcus marinus

query: To get a list of sequence names from an ACNUC data base...

read.abif: Read ABIF formatted files

read.alignment: Read aligned sequence files in mase, clustal, phylip, fasta...

readBins: Import GenMapper Bins configuration file

read.fasta: read FASTA formatted files

readfirstrec: Low level function to get the record count of the specified...

readPanels: Import GenMapper Panels configuration file

readsmj: Low level function to read ACNUC SMJYT index files

rearranged.oriloc: Detection of replication-associated effects on base...

recstat: Prediction of Coding DNA Sequences.

residuecount: Total number of residues in an ACNUC list

revaligntest: Three aligned nucleic acid sequences

reverse.align: Reverse alignment - from protein sequence alignment to...

rot13: Ergheaf gur EBG-13 pvcurevat bs n fgevat

s2c: conversion of a string into a vector of chars

s2n: simple numerical encoding of a DNA sequence.

savelist: Save sequence names or accession numbers into a file

SeqAcnucWeb: Sequence coming from a remote ACNUC data base

SeqFastaAA: AA sequence in Fasta Format

SeqFastadna: Class for DNA sequence in Fasta Format

SeqFrag: Class for sub-sequences

seqinr-package: Biological Sequences Retrieval and Analysis

SEQINR.UTIL: utility data for seqinr

setlistname: Sets the name of an ACNUC list identified by its rank

splitseq: split a sequence into sub-sequences

stresc: Utility function to escape LaTeX special characters present...

stutterabif: Stutter ratio estimation

swap: Exchange two R objects

syncodons: Synonymous codons

synsequence: Random synonymous coding sequence generation

tablecode: to plot genetic code as in textbooks Tests if regions located between Stop codons contain putative... Tests if regions located between Stop codons contain putative...

toyaa: A toy example of amino-acid counts in three proteins

toycodon: A toy example of codon counts in three coding sequences

translate: Translate nucleic acid sequences into proteins

trimSpace: Trim leading and/or trailing spaces in strings

uco: Codon usage indices

ucoweight: Weight of each synonymous codon

waterabs: Light absorption by the water column Scans databases for a given sequence accession number

words: To get all words from an alphabet.

words.pos: Positions of possibly degenerated motifs within sequences

write.fasta: Write sequence(s) into a file in fasta format

zscore: Statistical over- and under- representation of dinucleotides...


a Man page
aaa Man page
aacost Man page
aaindex Man page
AAstat Man page
acnucclose Man page
acnucopen Man page
al2bp Man page
alllistranks Man page
alr Man page
amb Man page
AnoukResult Man page
as.alignment Man page
as.matrix.alignment Man page
as.SeqAcnucWeb Man page
as.SeqFastaAA Man page
as.SeqFastadna Man page
as.SeqFrag Man page
autosocket Man page
baselineabif Man page
bma Man page
c2s Man page
cai Man page
caitab Man page
cfl Man page
chargaff Man page
choosebank Man page
circle Man page
clfcd Man page
clientid Man page
closebank Man page
clustal Man page
col2alpha Man page
comp Man page
computePI Man page
con Man page
consensus Man page
count Man page
countfreelists Man page
countsubseqs Man page
crelistfromclientdata Man page
css Man page
dia.bactgensize Man page
dia.db.growth Man page
dinucl Man page
dist.alignment Man page
dotchart.uco Man page
dotPlot Man page
draw.oriloc Man page
draw.rearranged.oriloc Man page
draw.recstat Man page
ec999 Man page
ECH Man page
EXP Man page
exseq Man page
extract.breakpoints Man page
extractseqs Man page
fasta Man page
FASTA Man page
fastacc Man page
gb2fasta Man page
gbk2g2 Man page
gbk2g2.euk Man page
GC Man page
GC1 Man page
GC2 Man page
GC3 Man page
gcO2 Man page
GCpos Man page
gcT Man page
getAnnot Man page
getAnnot.default Man page
getAnnot.list Man page
getAnnot.logical Man page
getAnnot.qaw Man page
getAnnot.SeqAcnucWeb Man page
getAnnot.SeqFastaAA Man page
getAnnot.SeqFastadna Man page
getAttributsocket Man page
get.db.growth Man page
getFrag Man page
getFrag.character Man page
getFrag.default Man page
getFrag.list Man page
getFrag.logical Man page
getFrag.qaw Man page
getFrag.SeqAcnucWeb Man page
getFrag.SeqFastaAA Man page
getFrag.SeqFastadna Man page
getFrag.SeqFrag Man page
getKeyword Man page
getKeyword.default Man page
getKeyword.list Man page
getKeyword.logical Man page
getKeyword.qaw Man page
getKeyword.SeqAcnucWeb Man page
getLength Man page
getLength.character Man page
getLength.default Man page
getLength.list Man page
getLength.logical Man page
getLength.qaw Man page
getLength.SeqAcnucWeb Man page
getLength.SeqFastaAA Man page
getLength.SeqFastadna Man page
getLength.SeqFrag Man page
getlistrank Man page
getliststate Man page
getLocation Man page
getLocation.default Man page
getLocation.list Man page
getLocation.logical Man page
getLocation.qaw Man page
getLocation.SeqAcnucWeb Man page
getName Man page
getName.default Man page
getName.list Man page
getName.logical Man page
getName.qaw Man page
getName.SeqAcnucWeb Man page
getName.SeqFastaAA Man page
getName.SeqFastadna Man page
getName.SeqFrag Man page
get.ncbi Man page
getNumber.socket Man page
getSequence Man page
getSequence.character Man page
getSequence.default Man page
getSequence.list Man page
getSequence.logical Man page
getSequence.qaw Man page
getSequence.SeqAcnucWeb Man page
getSequence.SeqFastaAA Man page
getSequence.SeqFastadna Man page
getSequence.SeqFrag Man page
getTrans Man page
getTrans.character Man page
getTrans.default Man page
getTrans.list Man page
getTrans.logical Man page
getTrans.qaw Man page
getTrans.SeqAcnucWeb Man page
getTrans.SeqFastadna Man page
getTrans.SeqFrag Man page
getType Man page
gfrag Man page
ghelp Man page
gln Man page
glr Man page
gls Man page
gs500liz Man page
identifiler Man page
isenum Man page
isn Man page
is.SeqAcnucWeb Man page
is.SeqFastaAA Man page
is.SeqFastadna Man page
is.SeqFrag Man page
JLO Man page
kaks Man page
kdb Man page
knowndbs Man page
lseqinr Man page
m16j Man page
mase Man page
modifylist Man page
move Man page
msf Man page
mv Man page
n2s Man page
ncbi.fna.url Man page
ncbi.gbk.url Man page
ncbi.ptt.url Man page
ncbi.stats Man page
oriloc Man page
parser.socket Man page
peakabif Man page
permutation Man page
pga Man page
phylip Man page
pK Man page
plotabif Man page
plotladder Man page
plotPanels Man page
plot.SeqAcnucWeb Man page
pmw Man page
prepgetannots Man page
prettyseq Man page
print.qaw Man page
print.SeqAcnucWeb Man page
prochlo Man page
query Man page
quitacnuc Man page
read.abif Man page
read.alignment Man page
readAnnots.socket Man page
readBins Man page
readfasta Man page
read.fasta Man page
readfirstrec Man page
readPanels Man page
readsmj Man page
rearranged.oriloc Man page
recstat Man page
residuecount Man page
revaligntest Man page
reverse.align Man page
rho Man page
rot13 Man page
rscu Man page
s2c Man page
s2n Man page
savelist Man page
SeqAcnucWeb Man page
SeqFastaAA Man page
SeqFastadna Man page
SeqFrag Man page
seqinr Man page
seqinr-package Man page
setlistname Man page
splitseq Man page
stresc Man page
stutterabif Man page
summary.SeqFastaAA Man page
summary.SeqFastadna Man page
swap Man page
syncodons Man page
synsequence Man page
tablecode Man page Man page Man page
toyaa Man page
toycodon Man page
translate Man page
trimSpace Man page
uco Man page
ucoweight Man page
waterabs Man page Man page
words Man page
words.pos Man page
write.fasta Man page
zscore Man page


R/getAnnot.R R/autosocket.R R/stresc.R R/setlistname.R R/gbk2g2.R R/getKeyword.R R/swap.R R/ghelp.R R/stutterabif.R R/cai.R R/choosebank.R R/closebank.R R/amb.R R/synonymous.R R/write.fasta.R R/splitseq.R R/dist.alignment.R R/plotladder.R R/zscore.R R/savelist.R R/rot13.R R/translate.R R/bma.R R/comp.R R/s2n.R R/db.growth.R R/pmw.R R/getFrag.R R/ClassSeq.R R/getLocation.R R/count.R R/R_socket.R R/dotchart.uco.R R/circle.R R/getlistrank.R R/GC.R R/as.matrix.alignment.R R/draw.oriloc.R R/readPanels.R R/ R/countfreelists.R R/fastacc.R R/read.fasta.R R/recstat.R R/allistranks.R R/gfrag.R R/move.R R/getTrans.R R/tablecode.R R/gbk2g2.euk.R R/AAstat.R R/draw.recstat.R R/query.r R/trimSpace.R R/acnucclose.R R/lseqinr.R R/getType.R R/draw.rearranged.oriloc.R R/getSequence.R R/reverse.align.R R/baselineabif.R R/peakabif.R R/plotPanels.R R/getLength.R R/readsmj.R R/rearranged.oriloc.R R/ R/prettyseq.R R/dotPlot.R R/prepgetannots.R R/getName.R R/acnucopen.R R/ R/modifylist.R R/read.alignment.R R/clfcd.R R/uco.R R/getliststate.R R/read.abif.R R/readfirstrec.R R/parser.socket.R R/knowndbs.R R/col2alpha.R R/isenum.R R/permutation.R R/util.R R/get.ncbi.R R/rho.R R/kaks.R R/al2bp.R R/as.alignment.R R/PI.R R/words.R R/plot.SeqAcnucWeb.R R/oriloc.R R/plotabif.R R/quitacnuc.R R/extract.breakpoints.R R/gb2fasta.R R/words.pos.R R/dia.bactgensize.R R/extractseqs.R R/readBins.R R/countsubseqs.R R/clientid.R R/residuecount.R R/consensus.R
man/mase.Rd man/aaa.Rd man/getFrag.Rd man/cai.Rd man/pmw.Rd man/SeqFastadna.Rd man/col2alpha.Rd man/SeqAcnucWeb.Rd man/waterabs.Rd man/words.Rd
man/msf.Rd man/prepgatannots.Rd man/phylip.Rd man/computePI.Rd man/ucoweight.Rd man/getLocation.Rd man/s2c.Rd man/AAstat.Rd man/gfrag.Rd man/modifylist.Rd man/ man/gcO2.Rd man/savelist.Rd man/parser.socket.Rd man/prettyseq.Rd man/stresc.Rd man/m16j.Rd man/plotPanels.Rd man/bma.Rd man/swap.Rd man/choosebank.Rd man/kaks.Rd man/pK.Rd man/readfirstrec.Rd man/getlistrank.Rd man/dotPlot.Rd man/read.fasta.Rd man/autosocket.Rd man/aacost.Rd man/toycodon.Rd man/trimSpace.Rd man/amb.Rd man/aaindex.Rd man/ghelp.Rd man/ man/n2s.Rd man/fasta.Rd man/alllistranks.Rd man/splitseq.Rd man/uco.Rd man/setlistname.Rd man/lseqinr.Rd man/fastacc.Rd man/chargaff.Rd man/zscore.Rd man/synsequence.Rd man/get.db.growth.Rd man/ECH.Rd man/dist.alignment.Rd man/seqinr-package.Rd man/getliststate.Rd man/EXP.Rd man/countfreelists.Rd man/dia.bactgensize.Rd man/get.ncbi.Rd man/comp.Rd man/draw.rearranged.oriloc.Rd man/print.SeqAcnucWeb.Rd man/draw.oriloc.Rd man/isenum.Rd man/rot13.Rd man/syncodons.Rd man/extract.breakpoints.Rd man/as.matrix.alignment.Rd man/baselineabif.Rd man/plotabif.Rd man/extractseqs.Rd man/getType.Rd man/AnoukResult.Rd man/read.abif.Rd man/plot.SeqAcnucWeb.Rd man/gbk2g2.Rd man/GC.Rd man/s2n.Rd man/translate.Rd man/acnucopen.Rd man/write.fasta.Rd man/dotchart.uco.Rd man/readsmj.Rd man/ man/consensus.Rd man/as.alignment.Rd man/plotladder.Rd man/stutterabif.Rd man/identifiler.Rd man/print.qaw.Rd man/closebank.Rd man/getTrans.Rd man/readBins.Rd man/ec999.Rd man/tablecode.Rd man/clustal.Rd man/gb2fasta.Rd man/c2s.Rd man/words.pos.Rd man/caitab.Rd man/countsubseqs.Rd man/permutation.Rd man/revaligntest.Rd man/SEQINR.UTIL.Rd man/crelistfromclientdata.Rd man/getKeyword.Rd man/prochlo.Rd man/query.Rd man/residuecount.Rd man/oriloc.Rd man/knowndbs.Rd man/dinucl.Rd man/gcT.Rd man/reverse.align.Rd man/peakabif.Rd man/count.Rd man/getAnnot.Rd man/SeqFastaAA.Rd man/move.Rd man/a.Rd man/al2bp.Rd man/rearranged.oriloc.Rd man/circle.Rd man/draw.recstat.Rd man/readPanels.Rd man/getSequence.Rd man/getName.Rd man/toyaa.Rd man/gbk2g2.euk.Rd man/gs500liz.Rd man/recstat.Rd man/JLO.Rd man/getLength.Rd man/SeqFrag.Rd man/read.alignment.Rd

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