BioMedR (version 1.2.1)

getProt: Retrieve Protein Sequence in various Formats from Databases

Description

Retrieve Protein Sequence in various Formats from Databases(BMgetDrug)

Retrieve Protein Sequence (FASTA Format) from the UniProt Database(BMgetProt...UinProt)

Retrieve Protein Sequence (FASTA Format) from the KEGG Database(BMgetProt...KEGG)

Retrieve Protein Sequence (PDB Format) from RCSB PDB(BMgetProt...RCSBPDB)

Usage

BMgetProt(id, from = c("uniprot", "kegg", "pdb"), type = c("fasta",
  "pdb", "aaseq"), parallel = 5)
BMgetProtFASTAUinProt(id, parallel = 5)
BMgetProtSeqUniProt(id, parallel = 5)
BMgetProtFASTAKEGG(id, parallel = 5)
BMgetProtSeqKEGG(id, parallel = 5)
BMgetProtPDBRCSBPDB(id, parallel = 5)
BMgetProtSeqRCSBPDB(id, parallel = 5)

Arguments

id

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

from

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

type

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

This function retrieves protein sequences (FASTA format) from the UniProt database.

This function retrieves protein sequences (FASTA format) from the KEGG database.

This function retrieves protein sequences (PDB format) from RCSB PDB.

References

UniProt. https://www.uniprot.org/

UniProt REST API Documentation. https://www.uniprot.org/faq/28

UniProt. https://www.uniprot.org/

UniProt REST API Documentation. https://www.uniprot.org/faq/28

See Also

See BMgetDrug for retrieving drug molecules from five databases.

Examples

# NOT RUN {
# BMgetProt
id = c('P00750', 'P00751', 'P00752')
BMgetProt(id, from = 'uniprot', type = 'aaseq')
# }
# NOT RUN {
# }
# NOT RUN {
# BMgetProtFASTAUinProt
id = c('P00750', 'P00751', 'P00752')
BMgetProtFASTAUinProt(id)
# }
# NOT RUN {
# }
# NOT RUN {
# BMgetProtSeqUniProt
id = c('P00750', 'P00751', 'P00752')
BMgetProtSeqUniProt(id)
# }
# NOT RUN {
# }
# NOT RUN {
#  BMgetProtFASTAKEGG
id = c('hsa:10161', 'hsa:10162')
BMgetProtFASTAKEGG(id)
# }
# NOT RUN {
# }
# NOT RUN {
# BMgetProtSeqKEG
id = c('hsa:10161', 'hsa:10162')
BMgetProtSeqKEGG(id)
# }
# NOT RUN {
# }
# NOT RUN {
# BMgetProtPDBRCSBPDB
id = c('4HHB', '4FF9')
BMgetProtPDBRCSBPDB(id)
# }
# NOT RUN {
# }
# NOT RUN {
# BMgetProtSeqRCSBPDB
id = c('4HHB', '4FF9')
BMgetProtSeqRCSBPDB(id)
# }
# NOT RUN {
# }