R: utility data for seqinr

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).

### 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: 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 3.4-5 Index]