seqinr v1.0-1

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seqinr

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

Functions in seqinr

Name Description
plot.SeqAcnucWeb To Plot Subsequences on the Parent Sequence
getAnnot Generic Function to obtain annotation for a sequence
a Converts amino-acid three-letter code into the one-letter one
EXP Vectors of coefficients to compute linear forms.
c2s conversion of a vector of chars into a string
invers invers
lseqinr To see what's inside the package seqinr
SeqFastadna Class for DNA sequence in Fasta Format
get.db.growth Get the exponential growth of nucleic acid database content
SeqAcnucWeb Sequence coming from an ACNUC data bases located on the web
kaks to Get an Estimation of Ka and Ks
computePI To Compute the Theoretical Isoelectric Point
GC2 Calculates the fractional GC2 content of nucleic acid sequences
s2n simple numerical encoding of a DNA sequence.
SeqFrag Class for sub-sequences
AAstat To Get Some Protein Statistics
dia.bactgensize Distribution of bacterial genome size from GOLD
count Composition of dimer/trimer/etc nucleotides
GC3 Calculates the fractional GC3 content of nucleic acid sequences
SeqFastaAA AA sequence in Fasta Format
tablecode to plot genetic code as in textbooks
n2s function to convert the numeric encoding of a DNA sequence into a vector of characters
choosebank To select a database structured under ACNUC and located on the web
oriloc Prediction of origin and terminus of replication in bacteria
ec999 999 coding sequences from E. coli
read.fasta Read file in fasta format
gb2fasta conversion of GenBank file into fasta file
getTrans Generic Function to translate a sequence
getLength Generic Function To obtain the length of a sequence
aaa Converts amino-acid one-letter code into the three-letter one
getType To Get Sequence Type
uco Create codon usage table
words.pos Positions of possibly degenerated motifs within sequences
dist.alignment Pairwise Distances from Aligned Protein or DNA/RNA Sequences
getSequence Generic Function To Get a sequence
translate Translate nucleic acid sequences
getKeyword Generic Function to get keyword(s) associated to a sequence
dotchart.uco Cleveland plot for codon usage tables
words To get all words from an alphabet.
chargaff Base composition in ssDNA for 7 bacterial DNA
getName Generic Function To obtain the name of a sequence
splitseq split a sequence into sub-sequences
SEQINR.UTIL utility data for seqinr
comp complement a nucleic sequence
read.alignment Read file in mase, clustal, phylip, fasta or msf format
gbk2g2 Conversion of a GenBank format file into a glimmer-like one
s2c conversion of a string into a vector of chars
get.ncbi Bacterial complete genome data from ncbi ftp site
GC Calculates the fractional GC content of nucleic acid sequences
getFrag Generic Function to obtain a fragment of a sequence
getLocation Generic Function To obtain the Position of a Sequence on the Parent Sequence
query To get a list of sequence names from an ACNUC data base located on the web
closebank To close a remote ACNUC database
dinucl Mean zscore on 242 complete bacterial chromosomes
aacost Aerobic cost of amino-acids in Escherichia coli and G+C classes
dotPlot Dot Plot Comparison of two sequences
AnoukResult Expected numeric results for Ka and Ks computation
prochlo Zscore on three strains of Prochlorococcus marinus
synsequence Random synonymous coding sequence generation
GetFromSequence Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence
dinucleotides Statistical over- and under- representation of dinucleotides in a sequence
permutation Sequence permutation according to several different models
ucoweight Weight of each synonymous codon
G+C Content Calculates the fractional G+C content of nucleic acid sequences
pmw Protein Molecular Weight
reverse.align Reverse alignment - from protein sequence alignment to nucleic sequence alignment
toyaa A toy example of amino-acid counts in three proteins
toycodon A toy example of codon counts in three coding sequences
crelistfromclientdata To create on server a bitlist from data lines sent by client
syncodons Synonymous codons
write.fasta Write file in fasta format
seqinr-package Biological Sequences Retrieval and Analysis
aaindex List of 544 physicochemical and biological properties for the 20 amino-acids
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Date 2005-02-16
License GPL version 2 or newer
URL http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_home.php, Mailing list: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr3_angl.php
Packaged Wed Feb 16 15:42:30 2005; delphine
Contributors Jean Lobry, Delphine Charif

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