env.extract: Sequence Environment Around a Given Position

In ptm: Analyses of Protein Post-Translational Modifications

Sequence Environment Around a Given Position

Description

Extracts the sequence environment around a given position.

Usage

env.extract(prot, db = 'none', c, r, ctr = 'none', exclude = c())

Arguments

prot	either a uniprot id or a string sequence.
db	a character string specifying the desired database; it must be one of 'uniprot', 'metosite', 'none'.
c	center of the environment.
r	radius of the environment.
ctr	the type of control environment; it must be one of 'random', 'closest', or 'none'.
exclude	a vector containing the positions to be excluded as control.

Details

The random control returns an environment center at a random position containing the same type or amino acid than the positive environment. The closest control searches for the closest position where such a type of amino acid is found and returns its environment.

Value

Returns a list of two strings (environments).

Author(s)

Juan Carlos Aledo

References

Aledo et al. Sci Rep. 2015; 5: 16955. (PMID: 26597773)

See Also

env.matrices(), env.Ztest() and env.plot()

Examples

env.extract('P01009', db = 'uniprot', 271, 10, ctr = 'random')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.