ptm (version 0.2.2)

get.seq: 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.

Value

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

Examples

# NOT RUN {
get.seq('P01009')
# }
# NOT RUN {
get.seq("hsa:5265", db = "kegg-aa")
# }
# NOT RUN {
get.seq("1u8f:P", db = "pdb")
# }