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.

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 publication2016-10-14 16:18:55
MaintainerSimon Penel <simon.penel@univ-lyon1.fr>
LicenseGPL (>= 2)
Version3.3-4
http://seqinr.r-forge.r-project.org/

View on R-Forge

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

test.co.recstat: Tests if regions located between Stop codons contain putative...

test.li.recstat: 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

where.is.this.acc: 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...

Files in this package

seqinr/DESCRIPTION
seqinr/NAMESPACE
seqinr/R
seqinr/R/AAstat.R seqinr/R/ClassSeq.R seqinr/R/GC.R seqinr/R/PI.R seqinr/R/R_socket.R seqinr/R/acnucclose.R seqinr/R/acnucopen.R seqinr/R/al2bp.R seqinr/R/allistranks.R seqinr/R/amb.R seqinr/R/as.alignment.R seqinr/R/as.matrix.alignment.R seqinr/R/autosocket.R seqinr/R/baselineabif.R seqinr/R/bma.R seqinr/R/cai.R seqinr/R/choosebank.R seqinr/R/circle.R seqinr/R/clfcd.R seqinr/R/clientid.R seqinr/R/closebank.R seqinr/R/col2alpha.R seqinr/R/comp.R seqinr/R/consensus.R seqinr/R/count.R seqinr/R/countfreelists.R seqinr/R/countsubseqs.R seqinr/R/db.growth.R seqinr/R/dia.bactgensize.R seqinr/R/dist.alignment.R seqinr/R/dotPlot.R seqinr/R/dotchart.uco.R seqinr/R/draw.oriloc.R seqinr/R/draw.rearranged.oriloc.R seqinr/R/draw.recstat.R seqinr/R/extract.breakpoints.R seqinr/R/extractseqs.R seqinr/R/fastacc.R seqinr/R/gb2fasta.R seqinr/R/gbk2g2.R seqinr/R/gbk2g2.euk.R seqinr/R/get.ncbi.R seqinr/R/getAnnot.R seqinr/R/getFrag.R seqinr/R/getKeyword.R seqinr/R/getLength.R seqinr/R/getLocation.R seqinr/R/getName.R seqinr/R/getSequence.R seqinr/R/getTrans.R seqinr/R/getType.R seqinr/R/getlistrank.R seqinr/R/getliststate.R seqinr/R/gfrag.R seqinr/R/ghelp.R seqinr/R/isenum.R seqinr/R/kaks.R seqinr/R/knowndbs.R seqinr/R/lseqinr.R seqinr/R/modifylist.R seqinr/R/move.R seqinr/R/oriloc.R seqinr/R/parser.socket.R seqinr/R/peakabif.R seqinr/R/permutation.R seqinr/R/plot.SeqAcnucWeb.R seqinr/R/plotPanels.R seqinr/R/plotabif.R seqinr/R/plotladder.R seqinr/R/pmw.R seqinr/R/prepgetannots.R seqinr/R/prettyseq.R
seqinr/R/query.r
seqinr/R/quitacnuc.R seqinr/R/read.abif.R seqinr/R/read.alignment.R seqinr/R/read.fasta.R seqinr/R/readBins.R seqinr/R/readPanels.R seqinr/R/readfirstrec.R seqinr/R/readsmj.R seqinr/R/rearranged.oriloc.R seqinr/R/recstat.R seqinr/R/residuecount.R seqinr/R/reverse.align.R seqinr/R/rho.R seqinr/R/rot13.R seqinr/R/s2n.R seqinr/R/savelist.R seqinr/R/setlistname.R seqinr/R/splitseq.R seqinr/R/stresc.R seqinr/R/stutterabif.R seqinr/R/swap.R seqinr/R/synonymous.R seqinr/R/tablecode.R seqinr/R/test.co.recstat.R seqinr/R/test.li.recstat.R seqinr/R/translate.R seqinr/R/trimSpace.R seqinr/R/uco.R seqinr/R/util.R seqinr/R/where.is.this.acc.R seqinr/R/words.R seqinr/R/words.pos.R seqinr/R/write.fasta.R seqinr/R/zscore.R
seqinr/data
seqinr/data/AnoukResult.RData
seqinr/data/ECH.RData
seqinr/data/EXP.RData
seqinr/data/JLO.RData
seqinr/data/SEQINR.UTIL.RData
seqinr/data/aacost.RData
seqinr/data/aaindex.RData
seqinr/data/caitab.RData
seqinr/data/chargaff.RData
seqinr/data/clustal.RData
seqinr/data/datalist
seqinr/data/dinucl.RData
seqinr/data/ec999.RData
seqinr/data/fasta.RData
seqinr/data/gcO2.rda
seqinr/data/gcT.rda
seqinr/data/gs500liz.RData
seqinr/data/identifiler.RData
seqinr/data/m16j.RData
seqinr/data/mase.RData
seqinr/data/msf.RData
seqinr/data/pK.RData
seqinr/data/phylip.RData
seqinr/data/prochlo.RData
seqinr/data/revaligntest.RData
seqinr/data/sysdata.rda
seqinr/data/toyaa.RData
seqinr/data/toycodon.RData
seqinr/data/waterabs.RData
seqinr/inst
seqinr/inst/CITATION
seqinr/inst/abif
seqinr/inst/abif/1_0000206138_C01_005.fsa
seqinr/inst/abif/1_FAC321_0000205983_B02_004.fsa
seqinr/inst/abif/2_0000206138_C01_005.fsa
seqinr/inst/abif/2_FAC321_0000205983_B02_004.fsa
seqinr/inst/abif/AmpFLSTR_Bins_v1.txt
seqinr/inst/abif/AmpFLSTR_Panels_v1.txt
seqinr/inst/abif/NGM_Bins.txt
seqinr/inst/abif/NGM_Pa.txt
seqinr/inst/abif/Promega_Bins_v1.txt
seqinr/inst/abif/Promega_Panels_v1.txt
seqinr/inst/abif/Prototype_PowerPlex_EP01_Bins.txt
seqinr/inst/abif/Prototype_PowerPlex_EP01_Pa.txt
seqinr/inst/abif/samplefsa2ps.fsa
seqinr/inst/sequences
seqinr/inst/sequences/Anouk.fasta
seqinr/inst/sequences/DarrenObbard.fasta
seqinr/inst/sequences/ECOUNC.fsa
seqinr/inst/sequences/UBIQUITIN.mase
seqinr/inst/sequences/ame1.gbk
seqinr/inst/sequences/bb.acc
seqinr/inst/sequences/bb.kwd
seqinr/inst/sequences/bb.mne
seqinr/inst/sequences/bb.sp
seqinr/inst/sequences/bordetella.fasta
seqinr/inst/sequences/bordetella.pep.aln
seqinr/inst/sequences/ct.bfa
seqinr/inst/sequences/ct.fasta.gz
seqinr/inst/sequences/ct.gbk.gz
seqinr/inst/sequences/ct.predict
seqinr/inst/sequences/ecolicgpe5.fasta
seqinr/inst/sequences/gopher.fasta
seqinr/inst/sequences/gopher.names
seqinr/inst/sequences/hannah.txt
seqinr/inst/sequences/humanMito.fasta
seqinr/inst/sequences/input.dat
seqinr/inst/sequences/input.out
seqinr/inst/sequences/legacy.fasta
seqinr/inst/sequences/louse.fasta
seqinr/inst/sequences/louse.names
seqinr/inst/sequences/malM.fasta
seqinr/inst/sequences/ortho.fasta
seqinr/inst/sequences/scuco.txt
seqinr/inst/sequences/seqAA.fasta
seqinr/inst/sequences/smallAA.fasta
seqinr/inst/sequences/smallAA.fasta.gz
seqinr/inst/sequences/someORF.fsa
seqinr/inst/sequences/test.aln
seqinr/inst/sequences/test.mase
seqinr/inst/sequences/test.msf
seqinr/inst/sequences/test.phylip
seqinr/man
seqinr/man/AAstat.Rd seqinr/man/AnoukResult.Rd seqinr/man/ECH.Rd seqinr/man/EXP.Rd seqinr/man/GC.Rd seqinr/man/JLO.Rd seqinr/man/SEQINR.UTIL.Rd seqinr/man/SeqAcnucWeb.Rd seqinr/man/SeqFastaAA.Rd seqinr/man/SeqFastadna.Rd seqinr/man/SeqFrag.Rd seqinr/man/a.Rd seqinr/man/aaa.Rd seqinr/man/aacost.Rd seqinr/man/aaindex.Rd seqinr/man/acnucopen.Rd seqinr/man/al2bp.Rd seqinr/man/alllistranks.Rd seqinr/man/amb.Rd seqinr/man/as.alignment.Rd seqinr/man/as.matrix.alignment.Rd seqinr/man/autosocket.Rd seqinr/man/baselineabif.Rd seqinr/man/bma.Rd seqinr/man/c2s.Rd seqinr/man/cai.Rd seqinr/man/caitab.Rd seqinr/man/chargaff.Rd seqinr/man/choosebank.Rd seqinr/man/circle.Rd seqinr/man/closebank.Rd seqinr/man/clustal.Rd seqinr/man/col2alpha.Rd seqinr/man/comp.Rd seqinr/man/computePI.Rd seqinr/man/consensus.Rd seqinr/man/count.Rd seqinr/man/countfreelists.Rd seqinr/man/countsubseqs.Rd seqinr/man/crelistfromclientdata.Rd seqinr/man/dia.bactgensize.Rd seqinr/man/dinucl.Rd seqinr/man/dist.alignment.Rd seqinr/man/dotPlot.Rd seqinr/man/dotchart.uco.Rd seqinr/man/draw.oriloc.Rd seqinr/man/draw.rearranged.oriloc.Rd seqinr/man/draw.recstat.Rd seqinr/man/ec999.Rd seqinr/man/extract.breakpoints.Rd seqinr/man/extractseqs.Rd seqinr/man/fasta.Rd seqinr/man/fastacc.Rd
seqinr/man/figures
seqinr/man/figures/aka.pdf
seqinr/man/figures/chargaff.png
seqinr/man/figures/gcskewmbe96.pdf
seqinr/man/figures/introduction-dbg.pdf
seqinr/man/figures/lncs2004.pdf
seqinr/man/figures/waterabs.jpg
seqinr/man/gb2fasta.Rd seqinr/man/gbk2g2.Rd seqinr/man/gbk2g2.euk.Rd seqinr/man/gcO2.Rd seqinr/man/gcT.Rd seqinr/man/get.db.growth.Rd seqinr/man/get.ncbi.Rd seqinr/man/getAnnot.Rd seqinr/man/getFrag.Rd seqinr/man/getKeyword.Rd seqinr/man/getLength.Rd seqinr/man/getLocation.Rd seqinr/man/getName.Rd seqinr/man/getSequence.Rd seqinr/man/getTrans.Rd seqinr/man/getType.Rd seqinr/man/getlistrank.Rd seqinr/man/getliststate.Rd seqinr/man/gfrag.Rd seqinr/man/ghelp.Rd seqinr/man/gs500liz.Rd seqinr/man/identifiler.Rd seqinr/man/isenum.Rd seqinr/man/kaks.Rd seqinr/man/knowndbs.Rd seqinr/man/lseqinr.Rd seqinr/man/m16j.Rd seqinr/man/mase.Rd seqinr/man/modifylist.Rd seqinr/man/move.Rd seqinr/man/msf.Rd seqinr/man/n2s.Rd seqinr/man/oriloc.Rd seqinr/man/pK.Rd seqinr/man/parser.socket.Rd seqinr/man/peakabif.Rd seqinr/man/permutation.Rd seqinr/man/phylip.Rd seqinr/man/plot.SeqAcnucWeb.Rd seqinr/man/plotPanels.Rd seqinr/man/plotabif.Rd seqinr/man/plotladder.Rd seqinr/man/pmw.Rd seqinr/man/prepgatannots.Rd seqinr/man/prettyseq.Rd seqinr/man/print.SeqAcnucWeb.Rd seqinr/man/print.qaw.Rd seqinr/man/prochlo.Rd seqinr/man/query.Rd seqinr/man/read.abif.Rd seqinr/man/read.alignment.Rd seqinr/man/read.fasta.Rd seqinr/man/readBins.Rd seqinr/man/readPanels.Rd seqinr/man/readfirstrec.Rd seqinr/man/readsmj.Rd seqinr/man/rearranged.oriloc.Rd seqinr/man/recstat.Rd seqinr/man/residuecount.Rd seqinr/man/revaligntest.Rd seqinr/man/reverse.align.Rd seqinr/man/rot13.Rd seqinr/man/s2c.Rd seqinr/man/s2n.Rd seqinr/man/savelist.Rd seqinr/man/seqinr-package.Rd seqinr/man/setlistname.Rd seqinr/man/splitseq.Rd seqinr/man/stresc.Rd seqinr/man/stutterabif.Rd seqinr/man/swap.Rd seqinr/man/syncodons.Rd seqinr/man/synsequence.Rd seqinr/man/tablecode.Rd seqinr/man/test.co.recstat.Rd seqinr/man/test.li.recstat.Rd seqinr/man/toyaa.Rd seqinr/man/toycodon.Rd seqinr/man/translate.Rd seqinr/man/trimSpace.Rd seqinr/man/uco.Rd seqinr/man/ucoweight.Rd seqinr/man/waterabs.Rd seqinr/man/where.is.this.acc.Rd seqinr/man/words.Rd seqinr/man/words.pos.Rd seqinr/man/write.fasta.Rd seqinr/man/zscore.Rd
seqinr/src
seqinr/src/Makevars
seqinr/src/Makevars.win
seqinr/src/alignment.c
seqinr/src/alignment.h
seqinr/src/fastacc.c
seqinr/src/getzlibsock.c
seqinr/src/kaks.c
seqinr/src/util.c
seqinr/src/zsockr.c

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