Use this function to search UniProt Archive (UniParc) entries.You may also refine your search with modifiers such as sequence length, taxon id etc. See "Arguments section" for more information.

rba_uniprot_uniparc_search(
  upi = NULL,
  accession = NULL,
  db_type = NULL,
  db_id = NULL,
  gene = NULL,
  protein = NULL,
  taxid = NULL,
  organism = NULL,
  sequence_checksum = NULL,
  ipr = NULL,
  signature_db = NULL,
  signature_id = NULL,
  upid = NULL,
  seq_length = NULL,
  rf_dd_type = NULL,
  rf_db_id = NULL,
  rf_active = NULL,
  rf_tax_id = NULL,
  ...
)

Arguments

upi

unique UniParc Identifier(s). You can supply up to 100 IDs.

accession

UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

db_type

cross-reference (external database) name.

db_id

Protein ID in the cross-reference (external) database. You can supply up to 100 IDs.

gene

UniProt gene name(s). You can supply up to 20 gene names.

protein

UniProt protein name.

taxid

NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

organism

Organism name.

sequence_checksum

Sequence CRC64 checksum.

ipr

InterPro identifier(s). You can supply up to 20 IDs.

signature_db

InterPro's signature database. You can supply up to 13 of the following values:
"CATH", "CDD", "HAMAP", "MobiDB Lite", "Panther", "Pfam", "PIRSF", "PRINTS", "Prosite", "SFLD", "SMART", "SUPERFAMILY" and/or "TIGRfams"

signature_id

Signature ID in the InterPro's signature database. You can supply up to 20 IDs.

upid

UniProt Proteome identifier (UPID). You can supply up to 100 UPIDs.

seq_length

An exact sequence length (e.g. 150) or a range of sequence lengths (e.g. "130-158").

rf_dd_type

Filter the content of the each UniParc entry by cross-reference names. You can supply multiple values.

rf_db_id

Filter the content of the each UniParc entry by protein identifiers in any cross-reference database. You can supply multiple values.

rf_active

(logical ) Filter the content of each UniParc entry based on active status on source database:

  • NULL: (default) don't filter contents based on active status.

  • TRUE: only return contents which are still active.

  • FALSE: Only return contents which are not active.

rf_tax_id

(Numeric) Filter the content of each UniParc entry by NIH-NCBI Taxon ID. You can supply multiple values.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A List where each element corresponds to one UniParc entry returned by your search query. The element itself is a sub-list containing sequence information and reference entries.

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/uniparc"

References

  • Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W539–W544, https://doi.org/10.1093/nar/gkx237

  • Proteins API Documentation

See also

Examples

# \donttest{
rba_uniprot_uniparc_search(upi = "UPI00000000C9")
# }
# \donttest{
rba_uniprot_uniparc_search(accession = "P30914")
# }
# \donttest{
rba_uniprot_uniparc_search(accession = "P30914", rf_active = TRUE)
# }
# \donttest{
rba_uniprot_uniparc_search(taxid = "694009", protein = "Nucleoprotein")
# }