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.

Author
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]
Date of publication
2016-10-14 16:18:55
Maintainer
Simon Penel <simon.penel@univ-lyon1.fr>
License
GPL (>= 2)
Version
3.3-4
URLs

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