Biological Sequences Retrieval and Analysis
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Documentation for package ‘seqinr’ version 4.2-36
Help Pages
A B C D E F G I J K L M N O P Q R S T U W Z misc
| seqinr-package | Biological Sequences Retrieval and Analysis |
-- A --
| 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 classes |
| aaindex | List of 544 physicochemical and biological properties for the 20 amino-acids |
| AAstat | To Get Some Protein Statistics |
| acnucclose | open and close a remote access to an ACNUC database |
| acnucopen | open and close a remote access to an ACNUC database |
| al2bp | To Convert a forensic microsatellite allele name into its length in base pairs |
| alllistranks | To get the count of existing lists and all their ranks on server |
| alr | To get the count of existing lists and all their ranks on server |
| 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 |
| as.SeqAcnucWeb | Sequence coming from a remote ACNUC data base |
| as.SeqFastaAA | AA sequence in Fasta Format |
| as.SeqFastadna | Class for DNA sequence in Fasta Format |
| as.SeqFrag | Class for sub-sequences |
| autosocket | Returns a socket to the last opened database |
-- B --
| baselineabif | Estimation of baseline value |
| bma | Computing an IUPAC nucleotide symbol |
-- C --
| c2s | conversion of a vector of chars into a string |
| cai | Codon Adaptation Index |
| caitab | Codon Adaptation Index (CAI) w tables |
| cfl | The number of free lists available and annotation lines in an ACNUC server |
| chargaff | Base composition in ssDNA for 7 bacterial DNA |
| choosebank | To select a database structured under ACNUC and located on the web |
| circle | Draws a circle |
| clfcd | To create on server an ACNUC list from data lines sent by client |
| clientid | open and close a remote access to an ACNUC database |
| 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 |
| con | Consensus and profiles for sequence alignments |
| 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 ACNUC server |
| countsubseqs | Number of subsequences in an ACNUC list |
| crelistfromclientdata | To create on server an ACNUC list from data lines sent by client |
| css | Number of subsequences in an ACNUC list |
-- D --
| dia.bactgensize | Distribution of bacterial genome size from GOLD |
| dia.db.growth | Get the exponential growth of nucleic acid database content |
| 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 chromosomes. |
| draw.rearranged.oriloc | Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes. |
| draw.recstat | Graphical representation of a recstat analysis. |
-- E --
| ec999 | 999 coding sequences from E. coli |
| ECH | Forensic Genetic Profile Allelic Ladder Raw Data |
| EXP | Vectors of coefficients to compute linear forms. |
| exseq | To extract the sequences information of a sequence or a list of sequence in different formats |
| extract.breakpoints | Extraction of breakpoint positions on the rearranged nucleotide skews. |
| extractseqs | To extract the sequences information of a sequence or a list of sequence in different formats |
-- F --
| FASTA | read FASTA formatted files |
| fasta | Example of results obtained after a call to read.alignment |
| fastacc | Fast Allele in Common Count |
-- G --
| 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. Eukaryotic version. |
| GC | Calculates the fractional G+C content of nucleic acid sequences. |
| GC1 | Calculates the fractional G+C content of nucleic acid sequences. |
| GC2 | Calculates the fractional G+C content of nucleic acid sequences. |
| GC3 | Calculates the fractional G+C content of nucleic acid sequences. |
| gcO2 | GC content and aerobiosis in bacteria |
| GCpos | Calculates the fractional G+C content of nucleic acid sequences. |
| gcT | GC content and temperature in bacteria |
| get.db.growth | Get the exponential growth of nucleic acid database content |
| getAnnot | Generic Function to get sequence annotations |
| getAnnot.default | Generic Function to get sequence annotations |
| getAnnot.list | Generic Function to get sequence annotations |
| getAnnot.logical | Generic Function to get sequence annotations |
| getAnnot.qaw | Generic Function to get sequence annotations |
| getAnnot.SeqAcnucWeb | Generic Function to get sequence annotations |
| getAnnot.SeqFastaAA | Generic Function to get sequence annotations |
| getAnnot.SeqFastadna | Generic Function to get sequence annotations |
| getAttributsocket | Get the ACNUC number of a sequence from its name or accession number |
| getFrag | Generic function to extract sequence fragments |
| getFrag.character | Generic function to extract sequence fragments |
| getFrag.default | Generic function to extract sequence fragments |
| getFrag.list | Generic function to extract sequence fragments |
| getFrag.logical | Generic function to extract sequence fragments |
| getFrag.qaw | Generic function to extract sequence fragments |
| getFrag.SeqAcnucWeb | Generic function to extract sequence fragments |
| getFrag.SeqFastaAA | Generic function to extract sequence fragments |
| getFrag.SeqFastadna | Generic function to extract sequence fragments |
| getFrag.SeqFrag | Generic function to extract sequence fragments |
| getKeyword | Generic function to get keywords associated to sequences |
| getKeyword.default | Generic function to get keywords associated to sequences |
| getKeyword.list | Generic function to get keywords associated to sequences |
| getKeyword.logical | Generic function to get keywords associated to sequences |
| getKeyword.qaw | Generic function to get keywords associated to sequences |
| getKeyword.SeqAcnucWeb | Generic function to get keywords associated to sequences |
| getLength | Generic function to get the length of sequences |
| getLength.character | Generic function to get the length of sequences |
| getLength.default | Generic function to get the length of sequences |
| getLength.list | Generic function to get the length of sequences |
| getLength.logical | Generic function to get the length of sequences |
| getLength.qaw | Generic function to get the length of sequences |
| getLength.SeqAcnucWeb | Generic function to get the length of sequences |
| getLength.SeqFastaAA | Generic function to get the length of sequences |
| getLength.SeqFastadna | Generic function to get the length of sequences |
| getLength.SeqFrag | 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 parent sequence |
| getLocation.default | Generic function to get the location of subsequences on the parent sequence |
| getLocation.list | Generic function to get the location of subsequences on the parent sequence |
| getLocation.logical | Generic function to get the location of subsequences on the parent sequence |
| getLocation.qaw | Generic function to get the location of subsequences on the parent sequence |
| getLocation.SeqAcnucWeb | Generic function to get the location of subsequences on the parent sequence |
| getName | Generic function to get the names of sequences |
| getName.default | Generic function to get the names of sequences |
| getName.list | Generic function to get the names of sequences |
| getName.logical | Generic function to get the names of sequences |
| getName.qaw | Generic function to get the names of sequences |
| getName.SeqAcnucWeb | Generic function to get the names of sequences |
| getName.SeqFastaAA | Generic function to get the names of sequences |
| getName.SeqFastadna | Generic function to get the names of sequences |
| getName.SeqFrag | Generic function to get the names of sequences |
| getNumber.socket | Get the ACNUC number of a sequence from its name or accession number |
| getSequence | Generic function to get sequence data |
| getSequence.character | Generic function to get sequence data |
| getSequence.default | Generic function to get sequence data |
| getSequence.list | Generic function to get sequence data |
| getSequence.logical | Generic function to get sequence data |
| getSequence.qaw | Generic function to get sequence data |
| getSequence.SeqAcnucWeb | Generic function to get sequence data |
| getSequence.SeqFastaAA | Generic function to get sequence data |
| getSequence.SeqFastadna | Generic function to get sequence data |
| getSequence.SeqFrag | Generic function to get sequence data |
| getTrans | Generic function to translate coding sequences into proteins |
| getTrans.character | Generic function to translate coding sequences into proteins |
| getTrans.default | Generic function to translate coding sequences into proteins |
| getTrans.list | Generic function to translate coding sequences into proteins |
| getTrans.logical | Generic function to translate coding sequences into proteins |
| getTrans.qaw | Generic function to translate coding sequences into proteins |
| getTrans.SeqAcnucWeb | Generic function to translate coding sequences into proteins |
| getTrans.SeqFastadna | Generic function to translate coding sequences into proteins |
| getTrans.SeqFrag | Generic function to translate coding sequences into proteins |
| getType | To get available subsequence types in an opened ACNUC database |
| gfrag | Extract sequence identified by name or by number from an ACNUC server |
| ghelp | Get help from an ACNUC server |
| gln | Asks for information about an ACNUC list of specified rank |
| glr | To get the rank of a list from its name |
| gls | Asks for information about an ACNUC list of specified rank |
| gs500liz | GS500LIZ size standards |
-- I --
| identifiler | Identifiler allele names |
| is.SeqAcnucWeb | Sequence coming from a remote ACNUC data base |
| is.SeqFastaAA | AA sequence in Fasta Format |
| is.SeqFastadna | Class for DNA sequence in Fasta Format |
| is.SeqFrag | Class for sub-sequences |
| isenum | Get the ACNUC number of a sequence from its name or accession number |
| isn | Get the ACNUC number of a sequence from its name or accession number |
-- J --
| JLO | Forensic Genetic Profile Raw Data |
-- K --
| kaks | Ka and Ks, also known as dn and ds, computation |
| kaksTorture | Expected numeric results for Ka and Ks in extreme cases |
| kdb | Description of databases known by an ACNUC server |
| knowndbs | Description of databases known by an ACNUC server |
-- L --
| lseqinr | To see what's inside the package seqinr |
-- M --
| 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 |
| mv | Rename an R object |
-- N --
| n2s | function to convert the numeric encoding of a DNA sequence into a vector of characters |
-- O --
| oriloc | Prediction of origin and terminus of replication in bacteria. |
-- P --
| parser.socket | Utility function to parse answers from an ACNUC server |
| peakabif | Extraction of Peak locations, Heights and Surfaces from ABIF data |
| permutation | Sequence permutation according to several different models |
| pga | Select annotation lines in an ACNUC database |
| phylip | Example of results obtained after a call to read.alignment |
| pK | pK values for the side chain of charged amino acids from various sources |
| plot.SeqAcnucWeb | To Plot Subsequences on the Parent Sequence |
| 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. |
| pmw | Protein Molecular Weight |
| prepgetannots | 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 |
-- Q --
| query | To get a list of sequence names from an ACNUC data base located on the web |
| quitacnuc | open and close a remote access to an ACNUC database |
-- R --
| read.abif | Read ABIF formatted files |
| read.alignment | Read aligned sequence files in mase, clustal, phylip, fasta or msf format |
| read.fasta | read FASTA formatted files |
| readAnnots.socket | Generic Function to get sequence annotations |
| readBins | Import GenMapper Bins configuration file |
| readfasta | read FASTA formatted files |
| readfirstrec | Low level function to get the record count of the specified ACNUC index file |
| 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 composition asymmetry in prokaryotic chromosomes. |
| 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 nucleic sequence alignment |
| rho | Statistical over- and under- representation of dinucleotides in a sequence |
| rot13 | Ergheaf gur EBG-13 pvcurevat bs n fgevat |
| rscu | Codon usage indices |
-- S --
| 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 | 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 in a string |
| stutterabif | Stutter ratio estimation |
| summary.SeqFastaAA | AA sequence in Fasta Format |
| summary.SeqFastadna | Class for DNA sequence in Fasta Format |
| swap | Exchange two R objects |
| syncodons | Synonymous codons |
| synsequence | Random synonymous coding sequence generation |
-- T --
| tablecode | to plot genetic code as in textbooks |
| 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. |
| 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 |
-- U --
| uco | Codon usage indices |
| ucoweight | Weight of each synonymous codon |
-- W --
| 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 |
-- Z --
| zscore | Statistical over- and under- representation of dinucleotides in a sequence |
-- misc --
| .seqinrEnv | To select a database structured under ACNUC and located on the web |