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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/ptmScan.R

Description

Scans the indicated protein in search of PTM sites.

Usage

1
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.

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.

Value

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

Author(s)

Juan Carlos Aledo

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

1
## Not run: ptm.scan('P01009', renumerate = TRUE)

ptm documentation built on May 24, 2021, 9:06 a.m.

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