seqinr (version 1.0-1)

SEQINR.UTIL: utility data for seqinr

Description

This data set gives the genetics code, the name of each codon, the IUPAC one-letter code for aminoacids and the physico-chemical class of amino acid and the pK values of amino acids described in Bjellqvist et al. (1993).

Usage

data(SEQINR.UTIL)

format

SEQINR.UTIL is a list containing the 4 following objects:

1. CODES.NCBI

{is a data frame containing the genetics code : The standard ('Universal') genetic code with a selection of non-standard codes. } CODON.AA{is a three columns data frame. The first column is a factor containing the codon. The second column is a factor giving the aminoacids names for each codon. The last column is a factor giving the IUPAC one-letter code for aminoacids} AA.PROPERTY{is a list giving the physico-chemical class of amino acid. The differents classes are the following one : Tiny, Small, Aliphatic, Aromatic, Non.polar, Polar, Charged, Basic, Acidic }

item

pK

emph

et al.

source

Data prepared by D.Charif [e-mail]. The genetic codes have been taken from the ncbi taxonomy database: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c. Last update October 05, 2000. The IUPAC one-letter code for aminoacids is descibed at: http://www.chem.qmul.ac.uk/iupac/AminoAcid/. pK values of amino acids were taken from Bjellqvist et al. Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F.(1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences.Electrophoresis, 14, 1023-1031. To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

Examples

data(SEQINR.UTIL)