Aligns multiple protein sequences.

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

msa function

<dl><dt>sequences</dt>
<dd>vector containing the sequences.</dd>
<dt>ids</dt>
<dd>vector containing the sequences' ids.</dd>
<dt>sfile</dt>
<dd>if different to FALSE, then it should be a string indicating the path where to save a fasta alignment file.</dd>
<dt>inhouse</dt>
<dd>logical, if TRUE the in-house MUSCLE software is used. It must be installed on your system and in the search path for executable.</dd></dl>

Arguments

Multiple Sequence Alignment — msa

<dl>

<dt>sequences</dt>
<dd>vector containing the sequences.</dd>


<dt>ids</dt>
<dd>vector containing the sequences' ids.</dd>


<dt>sfile</dt>
<dd>if different to FALSE, then it should be a string indicating the path where to save a fasta alignment file.</dd>


<dt>inhouse</dt>
<dd>logical, if TRUE the in-house MUSCLE software is used. It must be installed on your system and in the search path for executable.</dd>

</dl>

msa: Multiple Sequence Alignment

Description

Usage

Value

Arguments

References

See Also

Examples