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seqinr (version 3.1-2)

Biological Sequences Retrieval and Analysis

Description

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.

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Version

Install

install.packages('seqinr')

Monthly Downloads

19,283

Version

3.1-2

License

GPL (>= 2)

Maintainer

Simon Penel

Last Published

December 2nd, 2014

Functions in seqinr (3.1-2)

peakabif

Extraction of Peak locations, Heights and Surfaces from ABIF data
parser.socket

Utility function to parse answers from an ACNUC server
caitab

Codon Adaptation Index (CAI) w tables
comp

complements a nucleic acid sequence
readfirstrec

Low level function to get the record count of the specified ACNUC index file
prettyseq

Text representation of a sequence from an ACNUC server
readPanels

Import GenMapper Panels configuration file
alllistranks

To get the count of existing lists and all their ranks on server
as.matrix.alignment

as.matrix.alignment
dotPlot

Dot Plot Comparison of two sequences
splitseq

split a sequence into sub-sequences
baselineabif

Estimation of baseline value
consensus

Consensus and profiles for sequence alignments
count

Composition of dimer/trimer/etc oligomers
fastacc

Fast Allele in Common Count
AnoukResult

Expected numeric results for Ka and Ks computation
getType

To get available subsequence types in an opened ACNUC database
G+C Content

Calculates the fractional G+C content of nucleic acid sequences.
extractseqs

To extract the sequences information of a sequence or a list of sequence in different formats
SeqFrag

Class for sub-sequences
a

Converts amino-acid three-letter code into the one-letter one
closebank

To close a remote ACNUC database
getLength

Generic function to get the length of sequences
countsubseqs

Number of subsequences in an ACNUC list
gbk2g2.euk

Conversion of a GenBank format file into a glimmer-like one. Eukaryotic version.
oriloc

Prediction of origin and terminus of replication in bacteria.
aaindex

List of 544 physicochemical and biological properties for the 20 amino-acids
draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.
get.db.growth

Get the exponential growth of nucleic acid database content
ECH

Forensic Genetic Profile Allelic Ladder Raw Data
SeqAcnucWeb

Sequence coming from a remote ACNUC data base
recstat

Prediction of Coding DNA Sequences.
bma

Computing an IUPAC nucleotide symbol
getTrans

Generic function to translate coding sequences into proteins
SEQINR.UTIL

utility data for seqinr
computePI

To Compute the Theoretical Isoelectric Point
pmw

Protein Molecular Weight
plotabif

Electrophoregram plot for ABIF data
getKeyword

Generic function to get keywords associated to sequences
getName

Generic function to get the names of sequences
dia.bactgensize

Distribution of bacterial genome size from GOLD
test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.
getliststate

Asks for information about an ACNUC list of specified rank
plotPanels

Representation of Amplicon Size Ranges of a STR kit.
countfreelists

The number of free lists available and annotation lines in an ACNUC server
fasta

Example of results obtained after a call to read.alignment
draw.recstat

Graphical representation of a recstat analysis.
knowndbs

Description of databases known by an ACNUC server
m16j

Fragment of the E. coli chromosome
toycodon

A toy example of codon counts in three coding sequences
print.qaw

Print method for objects from class qaw
read.abif

Read ABIF formatted files
chargaff

Base composition in ssDNA for 7 bacterial DNA
autosocket

Returns a socket to the last opened database
draw.oriloc

Graphical representation for nucleotide skews in prokaryotic chromosomes.
trimSpace

Trim leading and/or trailing spaces in strings
col2alpha

To use a standard color with an alpha transparency chanel
readsmj

Low level function to read ACNUC SMJYT index files
lseqinr

To see what's inside the package seqinr
gbk2g2

Conversion of a GenBank format file into a glimmer-like one
plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence
getSequence

Generic function to get sequence data
gfrag

Extract sequence identified by name or by number from an ACNUC server
read.fasta

read FASTA formatted files
s2c

conversion of a string into a vector of chars
SeqFastadna

Class for DNA sequence in Fasta Format
aaa

Converts amino-acid one-letter code into the three-letter one
al2bp

To Convert a forensic microsatellite allele name into its length in base pairs
kaks

Ka and Ks, also known as dn and ds, computation
stutterabif

Stutter ratio estimation
words.pos

Positions of possibly degenerated motifs within sequences
JLO

Forensic Genetic Profile Raw Data
savelist

Save sequence names or accession numbers into a file
toyaa

A toy example of amino-acid counts in three proteins
prepgetannots

Select annotation lines in an ACNUC database
AAstat

To Get Some Protein Statistics
dotchart.uco

Cleveland plot for codon usage tables
gb2fasta

conversion of GenBank file into fasta file
as.alignment

Constructor for class alignment
ghelp

Get help from an ACNUC server
move

Rename an R object
get.ncbi

Bacterial complete genome data from ncbi ftp site
synsequence

Random synonymous coding sequence generation
syncodons

Synonymous codons
write.fasta

Write sequence(s) into a file in fasta format
read.alignment

Read aligned sequence files in mase, clustal, phylip, fasta or msf format
crelistfromclientdata

To create on server an ACNUC list from data lines sent by client
dinucleotides

Statistical over- and under- representation of dinucleotides in a sequence
query

To get a list of sequence names from an ACNUC data base located on the web
cai

Codon Adaptation Index
EXP

Vectors of coefficients to compute linear forms.
revaligntest

Three aligned nucleic acid sequences
tablecode

to plot genetic code as in textbooks
test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.
circle

Draws a circle
aacost

Aerobic cost of amino-acids in Escherichia coli and G+C classes
rot13

Ergheaf gur EBG-13 pvcurevat bs n fgevat
modifylist

Modification of an ACNUC list
plotladder

Simple plot of an allelic ladder from ABIF data
uco

Codon usage indices
reverse.align

Reverse alignment - from protein sequence alignment to nucleic sequence alignment
msf

Example of results obtained after a call to read.alignment
getlistrank

To get the rank of a list from its name
acnucopen

open and close a remote access to an ACNUC database
amb

Expansion of IUPAC nucleotide symbols
waterabs

Light absorption by the water column
isenum

Get the ACNUC number of a sequence from its name or accession number
print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb
readBins

Import GenMapper Bins configuration file
dist.alignment

Pairwise Distances from Aligned Protein or DNA/RNA Sequences
c2s

conversion of a vector of chars into a string
ucoweight

Weight of each synonymous codon
n2s

function to convert the numeric encoding of a DNA sequence into a vector of characters
clustal

Example of results obtained after a call to read.alignment
dinucl

Mean zscore on 242 complete bacterial chromosomes
pK

pK values for the side chain of charged amino acids from various sources
prochlo

Zscore on three strains of Prochlorococcus marinus
residuecount

Total number of residues in an ACNUC list
rearranged.oriloc

Detection of replication-associated effects on base composition asymmetry in prokaryotic chromosomes.
words

To get all words from an alphabet.
translate

Translate nucleic acid sequences into proteins
ec999

999 coding sequences from E. coli
seqinr-package

Biological Sequences Retrieval and Analysis
where.is.this.acc

Scans databases for a given sequence accession number
getAnnot

Generic Function to get sequence annotations
swap

Exchange two R objects
getFrag

Generic function to extract sequence fragments
setlistname

Sets the name of an ACNUC list identified by its rank
SeqFastaAA

AA sequence in Fasta Format
extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.
identifiler

Identifiler allele names
choosebank

To select a database structured under ACNUC and located on the web
getLocation

Generic function to get the location of subsequences on the parent sequence
gs500liz

GS500LIZ size standards
mase

Example of results obtained after a call to read.alignment
s2n

simple numerical encoding of a DNA sequence.
permutation

Sequence permutation according to several different models
stresc

Utility function to escape LaTeX special characters present in a string
phylip

Example of results obtained after a call to read.alignment