ptm (version 0.2.2)

ptm.scan: Scan a Protein in Search of PTM Sites

Description

Scans the indicated protein in search of PTM sites.

Usage

ptm.scan(up_id, renumerate = TRUE)

Arguments

up_id

a character string corresponding to the UniProt ID.

renumerate

logical, when TRUE the sequence numeration of MetO sites is that given by Uniprot, which may not coincide with that from MetOSite.

Value

Returns a dataframe where each row corresponds to a residue, and the columns inform about the modifications.

Details

The numerations of the sequences given by UniProt and MetOSite may or may not match. Sometimes one of the sequences corresponds to the precursor protein and the other to the processed mature protein.

References

Hornbeck et al. Nucleic Acids Res. 2019 47:D433-D441, (PMID: 30445427).

Huang et al. Nucleic Acids Res. 2019 47:D298-D308, (PMID: 30418626).

Ullah et al. Sci. Rep. 2016 6:23534, (PMID: 27010073).

Durek et al. Nucleic Acids Res.2010 38:D828-D834, (PMID: 19880383).

Dinkel et al. Nucleic Acids Res. 2011 39:D261-D567 (PMID: 21062810).

See Also

meto.scan(), ac.scan(), me.scan(), ub.scan(), su.scan(), gl.scan(), sni.scan(), ni.scan(), p.scan(), reg.scan(), dis.scan()

Examples

# NOT RUN {
ptm.scan('P01009', renumerate = TRUE)
# }