- seqinr: Biological Sequences Retrieval and Analysis
- SeqAcnucWeb: Sequence coming from a remote ACNUC data base
Sequence coming from a remote ACNUC data base
as.SeqAcnucWeb is called by many functions, for instance by
and should not be directly called by the user. It creates an object of class
is.SeqAcnucWeb returns TRUE if the object is of class
a string giving the name of a sequence present in the data base
a string giving the length of the sequence present in the data base
a string giving the frame of the sequence present in the data base
a string giving the ncbi genetic code of the sequence present in the data base
as.SeqAcnucWeb returns an object sequence of class
that as from seqinR 1.1-3 the slot socket has been deleted to save space for long lists.
D. Charif, J.R. Lobry
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- 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...