SEQINR.UTIL: utility data for seqinr
In seqinr: Biological Sequences Retrieval and Analysis

SEQINR.UTIL

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 amino acids and the physico-chemical class of amino acid and the pK values of amino acids described in Bjellqvist et al. (1993).

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.
The genetic codes have been taken from the ncbi database: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. Last visited on 2016-10-05 corresponding to last update of the Genetic Codes: April 30, 2013.
The IUPAC one-letter code for aminoacids is descibed at: https://www.bioinformatics.org/sms/iupac.html. 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.