seqinr v3.6-1

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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>.

Functions in seqinr

Name Description
AnoukResult Expected numeric results for Ka and Ks computation
ECH Forensic Genetic Profile Allelic Ladder Raw Data
SeqFastadna Class for DNA sequence in Fasta Format
JLO Forensic Genetic Profile Raw Data
AAstat To Get Some Protein Statistics
G+C Content Calculates the fractional G+C content of nucleic acid sequences.
SEQINR.UTIL utility data for seqinr
SeqFastaAA AA sequence in Fasta Format
EXP Vectors of coefficients to compute linear forms.
SeqAcnucWeb Sequence coming from a remote ACNUC data base
aaa Converts amino-acid one-letter code into the three-letter one
a Converts amino-acid three-letter code into the one-letter one
SeqFrag Class for sub-sequences
amb Expansion of IUPAC nucleotide symbols
as.alignment Constructor for class alignment
alllistranks To get the count of existing lists and all their ranks on server
al2bp To Convert a forensic microsatellite allele name into its length in base pairs
aaindex List of 544 physicochemical and biological properties for the 20 amino-acids
acnucopen open and close a remote access to an ACNUC database
baselineabif Estimation of baseline value
as.matrix.alignment as.matrix.alignment
choosebank To select a database structured under ACNUC and located on the web
aacost Aerobic cost of amino-acids in Escherichia coli and G+C classes
caitab Codon Adaptation Index (CAI) w tables
c2s conversion of a vector of chars into a string
bma Computing an IUPAC nucleotide symbol
autosocket Returns a socket to the last opened database
computePI To Compute the Theoretical Isoelectric Point
chargaff Base composition in ssDNA for 7 bacterial DNA
circle Draws a circle
count Composition of dimer/trimer/etc oligomers
dia.bactgensize Distribution of bacterial genome size from GOLD
countfreelists The number of free lists available and annotation lines in an ACNUC server
dinucl Mean zscore on 242 complete bacterial chromosomes
comp complements a nucleic acid sequence
col2alpha To use a standard color with an alpha transparency chanel
dotchart.uco Cleveland plot for codon usage tables
ec999 999 coding sequences from E. coli
countsubseqs Number of subsequences in an ACNUC list
crelistfromclientdata To create on server an ACNUC list from data lines sent by client
draw.oriloc Graphical representation for nucleotide skews in prokaryotic chromosomes.
get.db.growth Get the exponential growth of nucleic acid database content
draw.rearranged.oriloc Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.
consensus Consensus and profiles for sequence alignments
getName Generic function to get the names of sequences
getLocation Generic function to get the location of subsequences on the parent sequence
gb2fasta Conversion of GenBank file into fasta file
fastacc Fast Allele in Common Count
draw.recstat Graphical representation of a recstat analysis.
getKeyword Generic function to get keywords associated to sequences
getLength Generic function to get the length of sequences
extract.breakpoints Extraction of breakpoint positions on the rearranged nucleotide skews.
dist.alignment Pairwise Distances from Aligned Protein or DNA/RNA Sequences
cai Codon Adaptation Index
dotPlot Dot Plot Comparison of two sequences
gcT GC content and temperature in bacteria
gcO2 GC content and aerobiosis in bacteria
getliststate Asks for information about an ACNUC list of specified rank
closebank To close a remote ACNUC database
gfrag Extract sequence identified by name or by number from an ACNUC server
mase Example of results obtained after a call to read.alignment
m16j Fragment of the E. coli chromosome
n2s function to convert the numeric encoding of a DNA sequence into a vector of characters
msf Example of results obtained after a call to read.alignment
ghelp Get help from an ACNUC server
extractseqs To extract the sequences information of a sequence or a list of sequence in different formats
plotladder Simple plot of an allelic ladder from ABIF data
plotabif Electrophoregram plot for ABIF data
gs500liz GS500LIZ size standards
get.ncbi Bacterial complete genome data from ncbi ftp site
prettyseq Text representation of a sequence from an ACNUC server
move Rename an R object
modifylist Modification of an ACNUC list
print.SeqAcnucWeb Print method for objects from class SeqAcnucWeb
isenum Get the ACNUC number of a sequence from its name or accession number
getFrag Generic function to extract sequence fragments
identifiler Identifiler allele names
pK pK values for the side chain of charged amino acids from various sources
oriloc Prediction of origin and terminus of replication in bacteria.
getAnnot Generic Function to get sequence annotations
fasta Example of results obtained after a call to read.alignment
clustal Example of results obtained after a call to read.alignment
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. Eukaryotic version.
read.alignment Read aligned sequence files in mase, clustal, phylip, fasta or msf format
plotPanels Representation of Amplicon Size Ranges of a STR kit.
plot.SeqAcnucWeb To Plot Subsequences on the Parent Sequence
getSequence Generic function to get sequence data
readPanels Import GenMapper Panels configuration file
readBins Import GenMapper Bins configuration file
getTrans Generic function to translate coding sequences into proteins
permutation Sequence permutation according to several different models
savelist Save sequence names or accession numbers into a file
seqinr-package Biological Sequences Retrieval and Analysis
read.fasta read FASTA formatted files
kaks Ka and Ks, also known as dn and ds, computation
read.abif Read ABIF formatted files
rearranged.oriloc Detection of replication-associated effects on base composition asymmetry in prokaryotic chromosomes.
kaksTorture Expected numeric results for Ka and Ks in extreme cases
query To get a list of sequence names from an ACNUC data base located on the web
phylip Example of results obtained after a call to read.alignment
readsmj Low level function to read ACNUC SMJYT index files
readfirstrec Low level function to get the record count of the specified ACNUC index file
getType To get available subsequence types in an opened ACNUC database
getlistrank To get the rank of a list from its name
recstat Prediction of Coding DNA Sequences.
test.co.recstat Tests if regions located between Stop codons contain putative CDSs.
test.li.recstat Tests if regions located between Stop codons contain putative CDSs.
residuecount Total number of residues in an ACNUC list
revaligntest Three aligned nucleic acid sequences
setlistname Sets the name of an ACNUC list identified by its rank
s2n simple numerical encoding of a DNA sequence.
s2c conversion of a string into a vector of chars
synsequence Random synonymous coding sequence generation
knowndbs Description of databases known by an ACNUC server
splitseq split a sequence into sub-sequences
waterabs Light absorption by the water column
toycodon A toy example of codon counts in three coding sequences
toyaa A toy example of amino-acid counts in three proteins
swap Exchange two R objects
syncodons Synonymous codons
ucoweight Weight of each synonymous codon
uco Codon usage indices
where.is.this.acc Scans databases for a given sequence accession number
translate Translate nucleic acid sequences into proteins
tablecode to plot genetic code as in textbooks
trimSpace Trim leading and/or trailing spaces in strings
parser.socket Utility function to parse answers from an ACNUC server
lseqinr To see what's inside the package seqinr
write.fasta Write sequence(s) into a file in fasta format
pmw Protein Molecular Weight
print.qaw Print method for objects from class qaw
peakabif Extraction of Peak locations, Heights and Surfaces from ABIF data
prochlo Zscore on three strains of Prochlorococcus marinus
prepgetannots Select annotation lines in an ACNUC database
reverse.align Reverse alignment - from protein sequence alignment to nucleic sequence alignment
rot13 Ergheaf gur EBG-13 pvcurevat bs n fgevat
stresc Utility function to escape LaTeX special characters present in a string
stutterabif Stutter ratio estimation
words To get all words from an alphabet.
words.pos Positions of possibly degenerated motifs within sequences
dinucleotides Statistical over- and under- representation of dinucleotides in a sequence
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Encoding UTF-8
Date 2019-09-04
BugReports http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum
License GPL (>= 2)
SystemRequirements zlib headers and library.
URL http://seqinr.r-forge.r-project.org/
NeedsCompilation yes
Repository CRAN
Repository/R-Forge/Project seqinr
Repository/R-Forge/Revision 2100
Repository/R-Forge/DateTimeStamp 2019-09-04 11:36:47
Date/Publication 2019-09-07 17:30:06 UTC
Packaged 2019-09-04 12:10:08 UTC; rforge

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