get.seq

Imports a protein sequence from a selected database.

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'. 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.
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

get.seq function

<dl><dt>id</dt>
<dd>the identifier of the protein of interest.</dd>
<dt>db</dt>
<dd>a character string specifying the desired database; it must be one of 'uniprot' or 'metosite'.</dd>
<dt>as.string</dt>
<dd>logical, if TRUE the imported sequence will be returned as a character string.</dd></dl>

Arguments

Import a Protein Sequence from a Database — get.seq

<dl>

<dt>id</dt>
<dd>the identifier of the protein of interest.</dd>


<dt>db</dt>
<dd>a character string specifying the desired database; it must be one of 'uniprot' or 'metosite'.</dd>


<dt>as.string</dt>
<dd>logical, if TRUE the imported sequence will be returned as a character string.</dd>

</dl>

get.seq: Import a Protein Sequence from a Database

Description

Usage

Value

Arguments

Details

Examples