getProt: Retrieve Protein Sequence in various Formats from Databases

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

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.

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.

Value

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

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

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

# BMgetProt
id = c('P00750', 'P00751', 'P00752')
BMgetProt(id, from = 'uniprot', type = 'aaseq')


# BMgetProtFASTAUinProt
id = c('P00750', 'P00751', 'P00752')
BMgetProtFASTAUinProt(id)


# BMgetProtSeqUniProt
id = c('P00750', 'P00751', 'P00752')
BMgetProtSeqUniProt(id)


#  BMgetProtFASTAKEGG
id = c('hsa:10161', 'hsa:10162')
BMgetProtFASTAKEGG(id)


# BMgetProtSeqKEG
id = c('hsa:10161', 'hsa:10162')
BMgetProtSeqKEGG(id)


# BMgetProtPDBRCSBPDB
id = c('4HHB', '4FF9')
BMgetProtPDBRCSBPDB(id)


# BMgetProtSeqRCSBPDB
id = c('4HHB', '4FF9')
BMgetProtSeqRCSBPDB(id)

BioMedR documentation built on July 5, 2019, 9:03 a.m.