Biological Sequences Retrieval and Analysis


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Documentation for package ‘seqinr’ version 3.0-7

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A B C D E F G I J K L M N O P Q R S T U W Z

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.
GCpos Calculates the fractional G+C content of nucleic acid sequences.
get.db.growth Get the exponential growth of nucleic acid database content
get.ncbi Bacterial complete genome data from ncbi ftp site
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
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
ncbi.fna.url Bacterial complete genome data from ncbi ftp site
ncbi.gbk.url Bacterial complete genome data from ncbi ftp site
ncbi.ptt.url Bacterial complete genome data from ncbi ftp site
ncbi.stats Bacterial complete genome data from ncbi ftp site

-- 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