Retrieve Protein Sequence in various Formats from Databases

Retrieve Protein Sequence in various Formats from Databases

Usage

getProt(
  id,
  from = c("uniprot", "kegg", "pdb"),
  type = c("fasta", "pdb", "aaseq"),
  parallel = 5
)

Arguments

id

A character vector, as the protein ID(s).

from

The database, one of 'uniprot', 'kegg', or 'pdb'.

type

The returned protein format, one of fasta, pdb, or aaseq.

parallel

An integer, the parallel parameter, indicates how many process the user would like to use for retrieving the data (using RCurl), default is 5. For regular cases, we recommend a number less than 20.

Value

A length of id character list, each element containing the corresponding protein sequence(s) or file(s).

Details

This function retrieves protein sequence in various formats from three databases.

See also

See getDrug for retrieving drug molecules from five databases.

Examples

id = c('P00750', 'P00751', 'P00752')
# \donttest{
getProt(id, from = 'uniprot', type = 'aaseq')# }
#> [[1]]
#> [[1]]$`sp|P00750|TPA_HUMAN`
#> [1] "MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQHQSWLRPVLRSNRVEYCWCNSGRAQCHSVPVKSCSEPRCFNGGTCQQALYFSDFVCQCPEGFAGKCCEIDTRATCYEDQGISYRGTWSTAESGAECTNWNSSALAQKPYSGRRPDAIRLGLGNHNYCRNPDRDSKPWCYVFKAGKYSSEFCSTPACSEGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP"
#> 
#> 
#> [[2]]
#> [[2]]$`sp|P00751|CFAB_HUMAN`
#> [1] "MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVCPSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVSDEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDSVTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAEDGHGPGEQQKRKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL"
#> 
#> 
#> [[3]]
#> [[3]]$`sp|P00752|KLK_PIG`
#> [1] "APPIQSRIIGGRECEKNSHPWQVAIYHYSSFQCGGVLVNPKWVLTAAHCKNDNYEVWLGRHNLFENENTAQFFGVTADFPHPGFNLSLLKXHTKADGKDYSHDLMLLRLQSPAKITDAVKVLELPTQEPELGSTCEASGWGSIEPGPDBFEFPDEIQCVQLTLLQNTFCABAHPBKVTESMLCAGYLPGGKDTCMGDSGGPLICNGMWQGITSWGHTPCGSANKPSIYTKLIFYLDWINDTITENP"
#> 
#>