get.seq: Import a Protein Sequence from a Database

In ptm: Analyses of Protein Post-Translational Modifications

Import a Protein Sequence from a Database

Description

Imports a protein sequence from a selected database.

Usage

get.seq(id, db = 'uniprot', as.string = TRUE)

Arguments

id	the identifier of the protein of interest.
db	a character string specifying the desired database; it must be one of 'uniprot', 'metosite', 'pdb', 'kegg-aa', 'kegg-nt'.
as.string	logical, if TRUE the imported sequence will be returned as a character string.

Details

MetOSite uses the same type of protein ID than UniProt. However, if the chosen database is PDB, the identifier should be the 4-character unique identifier characteristic of PDB, followed by colon and the chain of interest. For instance, '2OCC:B' means we are interested in the sequence of chain B from the structure 2OCC. KEGG used its own IDs (see examples).

Value

Returns a protein (or nucleotide) sequence either as a character vector or a as a character string.

Author(s)

Juan Carlos Aledo

Examples

get.seq('P01009')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.