Man pages for seqinr
Biological Sequences Retrieval and Analysis

aConverts amino-acid three-letter code into the one-letter one
aaaConverts amino-acid one-letter code into the three-letter one
aacostAerobic cost of amino-acids in Escherichia coli and G+C...
aaindexList of 544 physicochemical and biological properties for the...
AAstatTo Get Some Protein Statistics
acnucopenopen and close a remote access to an ACNUC database
al2bpTo Convert a forensic microsatellite allele name into its...
alllistranksTo get the count of existing lists and all their ranks on...
ambExpansion of IUPAC nucleotide symbols
AnoukResultExpected numeric results for Ka and Ks computation
as.alignmentConstructor for class alignment
autosocketReturns a socket to the last opened database
baselineabifEstimation of baseline value
bmaComputing an IUPAC nucleotide symbol
c2sconversion of a vector of chars into a string
caiCodon Adaptation Index
caitabCodon Adaptation Index (CAI) w tables
chargaffBase composition in ssDNA for 7 bacterial DNA
choosebankTo select a database structured under ACNUC and located on...
circleDraws a circle
closebankTo close a remote ACNUC database
clustalExample of results obtained after a call to read.alignment
col2alphaTo use a standard color with an alpha transparency chanel
compcomplements a nucleic acid sequence
computePITo Compute the Theoretical Isoelectric Point
consensusConsensus and profiles for sequence alignments
countComposition of dimer/trimer/etc oligomers
countfreelistsThe number of free lists available and annotation lines in an...
countsubseqsNumber of subsequences in an ACNUC list
crelistfromclientdataTo create on server an ACNUC list from data lines sent by...
dia.bactgensizeDistribution of bacterial genome size from GOLD
dinuclMean zscore on 242 complete bacterial chromosomes
dist.alignmentPairwise Distances from Aligned Protein or DNA/RNA Sequences
dotchart.ucoCleveland plot for codon usage tables
dotPlotDot Plot Comparison of two sequences
draw.orilocGraphical representation for nucleotide skews in prokaryotic...
draw.rearranged.orilocGraphical representation for rearranged nucleotide skews in...
draw.recstatGraphical representation of a recstat analysis.
ec999999 coding sequences from E. coli
ECHForensic Genetic Profile Allelic Ladder Raw Data
EXPVectors of coefficients to compute linear forms.
extract.breakpointsExtraction of breakpoint positions on the rearranged...
extractseqsTo extract the sequences information of a sequence or a list...
fastaExample of results obtained after a call to read.alignment
fastaccFast Allele in Common Count
gb2fastaConversion of GenBank file into fasta file
gbk2g2Conversion of a GenBank format file into a glimmer-like one
gbk2g2.eukConversion of a GenBank format file into a glimmer-like one....
GCCalculates the fractional G+C content of nucleic acid...
gcO2GC content and aerobiosis in bacteria
gcTGC content and temperature in bacteria
getAnnotGeneric Function to get sequence annotations
get.db.growthGet the exponential growth of nucleic acid database content
getFragGeneric function to extract sequence fragments
getKeywordGeneric function to get keywords associated to sequences
getLengthGeneric function to get the length of sequences
getlistrankTo get the rank of a list from its name
getliststateAsks for information about an ACNUC list of specified rank
getLocationGeneric function to get the location of subsequences on the...
getNameGeneric function to get the names of sequences
get.ncbiBacterial complete genome data from ncbi ftp site
getSequenceGeneric function to get sequence data
getTransGeneric function to translate coding sequences into proteins
getTypeTo get available subsequence types in an opened ACNUC...
gfragExtract sequence identified by name or by number from an...
ghelpGet help from an ACNUC server
gs500lizGS500LIZ size standards
identifilerIdentifiler allele names
isenumGet the ACNUC number of a sequence from its name or accession...
JLOForensic Genetic Profile Raw Data
kaksKa and Ks, also known as dn and ds, computation
kaks-tortureExpected numeric results for Ka and Ks in extreme cases
knowndbsDescription of databases known by an ACNUC server
lseqinrTo see what's inside the package seqinr
m16jFragment of the E. coli chromosome
maseExample of results obtained after a call to read.alignment
modifylistModification of an ACNUC list
moveRename an R object
msfExample of results obtained after a call to read.alignment
n2sfunction to convert the numeric encoding of a DNA sequence...
orilocPrediction of origin and terminus of replication in bacteria.
parser.socketUtility function to parse answers from an ACNUC server
peakabifExtraction of Peak locations, Heights and Surfaces from ABIF...
permutationSequence permutation according to several different models
phylipExample of results obtained after a call to read.alignment
pKpK values for the side chain of charged amino acids from...
plotabifElectrophoregram plot for ABIF data
plotladderSimple plot of an allelic ladder from ABIF data
plotPanelsRepresentation of Amplicon Size Ranges of a STR kit.
plot.SeqAcnucWebTo Plot Subsequences on the Parent Sequence
pmwProtein Molecular Weight
prepgatannotsSelect annotation lines in an ACNUC database
prettyseqText representation of a sequence from an ACNUC server
print.qawPrint method for objects from class qaw
print.SeqAcnucWebPrint method for objects from class SeqAcnucWeb
prochloZscore on three strains of Prochlorococcus marinus
queryTo get a list of sequence names from an ACNUC data base...
read.abifRead ABIF formatted files
read.alignmentRead aligned sequence files in mase, clustal, phylip, fasta...
readBinsImport GenMapper Bins configuration file
read.fastaread FASTA formatted files
readfirstrecLow level function to get the record count of the specified...
readPanelsImport GenMapper Panels configuration file
readsmjLow level function to read ACNUC SMJYT index files
rearranged.orilocDetection of replication-associated effects on base...
recstatPrediction of Coding DNA Sequences.
residuecountTotal number of residues in an ACNUC list
revaligntestThree aligned nucleic acid sequences
reverse.alignReverse alignment - from protein sequence alignment to...
rot13Ergheaf gur EBG-13 pvcurevat bs n fgevat
s2cconversion of a string into a vector of chars
s2nsimple numerical encoding of a DNA sequence.
savelistSave sequence names or accession numbers into a file
SeqAcnucWebSequence coming from a remote ACNUC data base
SeqFastaAAAA sequence in Fasta Format
SeqFastadnaClass for DNA sequence in Fasta Format
SeqFragClass for sub-sequences
seqinr-packageBiological Sequences Retrieval and Analysis
SEQINR.UTILutility data for seqinr
setlistnameSets the name of an ACNUC list identified by its rank
splitseqsplit a sequence into sub-sequences
strescUtility function to escape LaTeX special characters present...
stutterabifStutter ratio estimation
swapExchange two R objects
syncodonsSynonymous codons
synsequenceRandom synonymous coding sequence generation
tablecodeto plot genetic code as in textbooks if regions located between Stop codons contain putative... if regions located between Stop codons contain putative...
toyaaA toy example of amino-acid counts in three proteins
toycodonA toy example of codon counts in three coding sequences
translateTranslate nucleic acid sequences into proteins
trimSpaceTrim leading and/or trailing spaces in strings
ucoCodon usage indices
ucoweightWeight of each synonymous codon
waterabsLight absorption by the water column databases for a given sequence accession number
wordsTo get all words from an alphabet.
words.posPositions of possibly degenerated motifs within sequences
write.fastaWrite sequence(s) into a file in fasta format
zscoreStatistical over- and under- representation of dinucleotides...
seqinr documentation built on Aug. 1, 2017, 5:01 p.m.