R: Biological Sequences Retrieval and Analysis

# Biological Sequences Retrieval and Analysis

## Documentation for package ‘seqinr’ version 3.4-5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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.
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
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
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
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