# Biological Sequences Retrieval and Analysis

## Documentation for package `seqinr' version 1.0-4

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- 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
AAstat | To Get Some Protein Statistics
AnoukResult | Expected numeric results for Ka and Ks computation
as.SeqAcnucWeb | Sequence coming from an ACNUC data bases located on the web
as.SeqFastaAA | AA sequence in Fasta Format
as.SeqFastadna | Class for DNA sequence in Fasta Format
as.SeqFrag | Class for sub-sequences

## -- C --

c2s | conversion of a vector of chars into a string
chargaff | Base composition in ssDNA for 7 bacterial DNA
choosebank | To select a database structured under ACNUC and located on the web
closebank | To close a remote ACNUC database
comp | complement a nucleic sequence
computePI | To Compute the Theoretical Isoelectric Point
count | Composition of dimer/trimer/etc nucleotides

## -- 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

## -- E --

ec999 | 999 coding sequences from E. coli
EXP | Vectors of coefficients to compute linear forms.

## -- G --

gb2fasta | conversion of GenBank file into fasta file
gbk2g2 | Conversion of a GenBank format file into a glimmer-like one
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
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 obtain annotation for a sequence
getAnnots | Generic Function to obtain annotation for a sequence
getAttributsocket | Generic Function To obtain the length of a sequence
getExon | Generic Function To obtain the Position of a Sequence on the Parent Sequence
getFrag | Generic Function to obtain a fragment of a sequence
getKeyword | Generic Function to get keyword(s) associated to a sequence
getKeywordsocket | Generic Function to get keyword(s) associated to a sequence
getLength | Generic Function To obtain the length of a sequence
getLocation | Generic Function To obtain the Position of a Sequence on the Parent Sequence
getLocationSocket | Generic Function To obtain the Position of a Sequence on the Parent Sequence
getName | Generic Function To obtain the name of a sequence
getNumber.socket | Generic Function To Get a sequence
getSequence | Generic Function To Get a sequence
getSequenceSocket | Generic Function To Get a sequence
getTrans | Generic Function to translate a sequence
getType | To Get Sequence Type

## -- I --

invers | invers
is.SeqAcnucWeb | Sequence coming from an ACNUC data bases located on the web
is.SeqFastaAA | AA sequence in Fasta Format
is.SeqFastadna | Class for DNA sequence in Fasta Format
is.SeqFrag | Class for sub-sequences

## -- K --

kaks | to Get an Estimation of Ka and Ks

## -- L --

lseqinr | To see what's inside the package seqinr

## -- 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 | Sequence coming from an ACNUC data bases located on the web
permutation | Sequence permutation according to several different models
plot.SeqAcnucWeb | To Plot Subsequences on the Parent Sequence
print.qaw | To get a list of sequence names from an ACNUC data base located on the web
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

## -- R --

read.alignment | Read aligned sequence files in mase, clustal, phylip, fasta or msf format
read.fasta | Read file in fasta format
readAnnots.socket | Generic Function to obtain annotation for a sequence
removeTrailingSpaces | To select a database structured under ACNUC and located on the web
rho | Statistical over- and under- representation of dinucleotides in a sequence

## -- S --

s2c | conversion of a string into a vector of chars
s2n | simple numerical encoding of a DNA sequence.
SeqAcnucWeb | Sequence coming from an ACNUC data bases located on the web
SeqFastaAA | AA sequence in Fasta Format
SeqFastadna | Class for DNA sequence in Fasta Format
SeqFrag | Class for sub-sequences
SEQINR.UTIL | utility data for seqinr
simon | To get a list of sequence names from an ACNUC data base located on the web
splitseq | split a sequence into sub-sequences
summary.SeqFastaAA | AA sequence in Fasta Format
summary.SeqFastadna | Class for DNA sequence in Fasta Format
syncodons | Synonymous codons
synsequence | Random synonymous coding sequence generation

## -- T --

tablecode | to plot genetic code as in textbooks
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

## -- U --

uco | Codon usage indices
ucoweight | Weight of each synonymous codon

## -- W --

words | To get all words from an alphabet.
words.pos | Positions of possibly degenerated motifs within sequences

## -- Z --

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