Biological Sequences Retrieval and Analysis


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Documentation for package `seqinr' version 1.0-6

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A C D E G I K L 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
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 complements a nucleic acid sequence
computePI To Compute the Theoretical Isoelectric Point
count Composition of dimer/trimer/etc nucleotides
crelistfromclientdata To create on server a bitlist from data lines sent by client

-- 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

-- 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 Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getAnnots Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getAttributsocket Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getExon Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getFrag Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getKeyword Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getKeywordsocket Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getLength Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getLocation Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getLocationSocket Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getName Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getNumber.socket Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getSequence Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getSequenceSocket Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
getTrans Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for 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
pmw Protein Molecular Weight
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 FASTA formatted files
readAnnots.socket Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
removeTrailingSpaces To select a database structured under ACNUC and located on the web
reverse.align Reverse alignment - from protein sequence alignment to nucleic sequence alignment
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 Biological Sequences Retrieval and Analysis
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
write.fasta Write file in fasta format

-- Z --

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