SEQINR.UTIL {seqinr}R Documentation

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:

    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
pK
is a data frame. It gives the pK values of amino acids described in Bjellqvist et al. (1993) , which were defined by examining polypeptide migration between pH 4.5 to 7.3 in an immobilised pH gradient gel environment with 9.2M and 9.8M urea at 15 degree or 25 degree

Source

Data prepared by D.Charif charif@biomserv.univ-lyon1.fr.
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.

References

citation("seqinr")

Examples

data(SEQINR.UTIL)

[Package seqinr version 1.1-6 Index]