env.extract

Extracts the sequence environment around a given position.

Contains utilities for the analysis of post-translational modifications (PTMs) in proteins,
with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download,
filter and analyze data from the sulfoxidation database 'MetOSite', and integrate data from other main PTMs
(other databases). Utilities to search and characterize S-aromatic motifs in proteins are also provided.
In addition, functions to analyze sequence environments around modifiable residues in proteins can be found.
For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable
residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
these differential sequence environments are also implemented. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).

Juan Aledo

Analyses of Protein Post-Translational Modifications

Juan Carlos Aledo

env.extract function

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

Arguments

Author

Sequence Environment Around a Given Position — env.extract

<dl>

<dt>prot</dt>
<dd>either a uniprot id or a string sequence.</dd>


<dt>db</dt>
<dd>a character string specifying the desired database; it must be one of 'uniprot', 'metosite', 'none'.</dd>


<dt>c</dt>
<dd>center of the environment.</dd>


<dt>r</dt>
<dd>radius of the environment.</dd>


<dt>ctr</dt>
<dd>the type of control environment; it must be one of 'random', 'closest', or 'none'.</dd>


<dt>exclude</dt>
<dd>a vector containing the positions to be excluded as control.</dd>

</dl>

env.extract: Sequence Environment Around a Given Position

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples