seqinr package - RDocumentation

alllistranks

To get the count of existing lists and all their ranks on server

aaa

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

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

aacost

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

AnoukResult

Expected numeric results for Ka and Ks computation

AAstat

To Get Some Protein Statistics

a

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

amb

Expansion of IUPAC nucleotide symbols

aaindex

List of 544 physicochemical and biological properties for the 20 amino-acids

bma

Computing an IUPAC nucleotide symbol

autosocket

Returns a socket to the last opened database

caitab

Codon Adaptation Index (CAI) w tables

chargaff

Base composition in ssDNA for 7 bacterial DNA

cai

Codon Adaptation Index

c2s

conversion of a vector of chars into a string

choosebank

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

as.matrix.alignment

as.alignment

Constructor for class alignment

baselineabif

Estimation of baseline value

comp

complements a nucleic acid sequence

clustal

Example of results obtained after a call to read.alignment

countfreelists

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

col2alpha

To use a standard color with an alpha transparency chanel

consensus

Consensus and profiles for sequence alignments

countsubseqs

Number of subsequences in an ACNUC list

circle

Draws a circle

computePI

To Compute the Theoretical Isoelectric Point

closebank

To close a remote ACNUC database

count

Composition of dimer/trimer/etc oligomers

dia.bactgensize

Distribution of bacterial genome size from GOLD

draw.recstat

Graphical representation of a recstat analysis.

dotPlot

Dot Plot Comparison of two sequences

ec999

999 coding sequences from E. coli

dinucl

Mean zscore on 242 complete bacterial chromosomes

crelistfromclientdata

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

dist.alignment

Pairwise Distances from Aligned Protein or DNA/RNA Sequences

draw.oriloc

Graphical representation for nucleotide skews in prokaryotic chromosomes.

dotchart.uco

Cleveland plot for codon usage tables

draw.rearranged.oriloc

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

gbk2g2.euk

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

ECH

Forensic Genetic Profile Allelic Ladder Raw Data

gb2fasta

Conversion of GenBank file into fasta file

EXP

Vectors of coefficients to compute linear forms.

extractseqs

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

fastacc

Fast Allele in Common Count

extract.breakpoints

Extraction of breakpoint positions on the rearranged nucleotide skews.

gbk2g2

Conversion of a GenBank format file into a glimmer-like one

G+C Content

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

fasta

Example of results obtained after a call to read.alignment

getAnnot

Generic Function to get sequence annotations

getliststate

Asks for information about an ACNUC list of specified rank

getlistrank

To get the rank of a list from its name

gcT

GC content and temperature in bacteria

gcO2

GC content and aerobiosis in bacteria

getFrag

Generic function to extract sequence fragments

getKeyword

Generic function to get keywords associated to sequences

get.ncbi

Bacterial complete genome data from ncbi ftp site

get.db.growth

Get the exponential growth of nucleic acid database content

getLength

Generic function to get the length of sequences

ghelp

Get help from an ACNUC server

gs500liz

GS500LIZ size standards

modifylist

Modification of an ACNUC list

move

Rename an R object

oriloc

Prediction of origin and terminus of replication in bacteria.

parser.socket

Utility function to parse answers from an ACNUC server

read.fasta

read FASTA formatted files

readBins

Import GenMapper Bins configuration file

getLocation

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

getName

Generic function to get the names of sequences

JLO

Forensic Genetic Profile Raw Data

kaks

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

pK

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

phylip

Example of results obtained after a call to read.alignment

prochlo

Zscore on three strains of Prochlorococcus marinus

query

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

reverse.align

Reverse alignment - from protein sequence alignment to nucleic sequence alignment

revaligntest

Three aligned nucleic acid sequences

residuecount

Total number of residues in an ACNUC list

recstat

Prediction of Coding DNA Sequences.

SeqAcnucWeb

Sequence coming from a remote ACNUC data base

SeqFastaAA

AA sequence in Fasta Format

synsequence

Random synonymous coding sequence generation

tablecode

to plot genetic code as in textbooks

translate

Translate nucleic acid sequences into proteins

getTrans

Generic function to translate coding sequences into proteins

getSequence

Generic function to get sequence data

trimSpace

Trim leading and/or trailing spaces in strings

n2s

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

msf

Example of results obtained after a call to read.alignment

peakabif

Extraction of Peak locations, Heights and Surfaces from ABIF data

permutation

Sequence permutation according to several different models

setlistname

Sets the name of an ACNUC list identified by its rank

stresc

Utility function to escape LaTeX special characters present in a string

splitseq

split a sequence into sub-sequences

stutterabif

Stutter ratio estimation

words

To get all words from an alphabet.

words.pos

Positions of possibly degenerated motifs within sequences

getType

To get available subsequence types in an opened ACNUC database

gfrag

Extract sequence identified by name or by number from an ACNUC server

lseqinr

To see what's inside the package seqinr

knowndbs

Description of databases known by an ACNUC server

plotabif

Electrophoregram plot for ABIF data

plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

prettyseq

Text representation of a sequence from an ACNUC server

prepgetannots

Select annotation lines in an ACNUC database

identifiler

Identifiler allele names

s2c

conversion of a string into a vector of chars

rot13

Ergheaf gur EBG-13 pvcurevat bs n fgevat

isenum

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

mase

Example of results obtained after a call to read.alignment

m16j

Fragment of the E. coli chromosome

readfirstrec

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

read.alignment

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

read.abif

Read ABIF formatted files

readPanels

Import GenMapper Panels configuration file

SeqFastadna

Class for DNA sequence in Fasta Format

plotladder

Simple plot of an allelic ladder from ABIF data

SeqFrag

Class for sub-sequences

plotPanels

Representation of Amplicon Size Ranges of a STR kit.

print.qaw

Print method for objects from class qaw

rearranged.oriloc

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

readsmj

Low level function to read ACNUC SMJYT index files

print.SeqAcnucWeb

Print method for objects from class SeqAcnucWeb

seqinr-package

Biological Sequences Retrieval and Analysis

SEQINR.UTIL

utility data for seqinr

toycodon

A toy example of codon counts in three coding sequences

toyaa

A toy example of amino-acid counts in three proteins

s2n

simple numerical encoding of a DNA sequence.

savelist

Save sequence names or accession numbers into a file

uco

Codon usage indices

test.li.recstat

Tests if regions located between Stop codons contain putative CDSs.

test.co.recstat

Tests if regions located between Stop codons contain putative CDSs.

swap

Exchange two R objects

waterabs

Light absorption by the water column

ucoweight

Weight of each synonymous codon

syncodons

Synonymous codons

dinucleotides

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

where.is.this.acc

Scans databases for a given sequence accession number

write.fasta

Write sequence(s) into a file in fasta format

seqinr (version 3.3-3)

Biological Sequences Retrieval and Analysis

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Functions in seqinr (3.3-3)