uniprot
Fetches UniProt entries based on their accession numbers.
The uniprot
command takes one or more UniProt accession numbers and returns the corresponding UniProt entry for each of the accession numbers as output. This information is fetched by using the UniProt webservice.
Input
The uniprot
command expects UniProt accession numbers as input. The source of this input can be command line arguments or standard input. If input is supplied using multiple sources at the same time, the order of priority as described above is used.
Command line arguments
If input is supplied using command line arguments, the accession numbers must be separated by spaces.
Example
$ uniprot C6JD41 Q06JG4 MTLVPLGDRVVLKQVEAEETTKSGIVLPGQAQEKPQQAEVVAVGPGGVVDGKEVKMEVAVGDKVIYSKYSGTEVKMDGTEYIIVKQNDILAIVK MFTNSIKNLIIYLMPLMVTLMLLSVSFVDAGKKPSGPNPGGNN
Standard input
If the command is run without arguments, uniprot
will read its input from standard input. When standard input is used, a single UniProt accession number per line is expected.
Example
$ cat input.txt C6JD41 Q06JG4 $ cat input | uniprot MTLVPLGDRVVLKQVEAEETTKSGIVLPGQAQEKPQQAEVVAVGPGGVVDGKEVKMEVAVGDKVIYSKYSGTEVKMDGTEYIIVKQNDILAIVK MFTNSIKNLIIYLMPLMVTLMLLSVSFVDAGKKPSGPNPGGNN
Output
The uniprot
command outputs the UniProt entry for each of the input accession numbers. By default, only the protein sequences are returned. By using the --format parameter, this can be changed to fasta, txt, xml, rdf or gff. All output is written to standard output.
Command-line options
--format / -f Specify the output format
By default, the uniprot
command only returns the protein sequence of the UniProt entry. The --format
option allows you to select another format. Supported formats are sequence, fasta, txt, xml, rdf, and gff.
Example
$ uniprot --format fasta C6JD41 Q06JG4 >tr|C6JD41|C6JD41_9FIRM 10 kDa chaperonin OS=Ruminococcus sp. 5_1_39BFAA GN=groS PE=3 SV=1 MTLVPLGDRVVLKQVEAEETTKSGIVLPGQAQEKPQQAEVVAVGPGGVVDGKEVKMEVAV GDKVIYSKYSGTEVKMDGTEYIIVKQNDILAIVK >sp|Q06JG4|16D10_MELHA CLAVATA3/ESR (CLE)-related protein 16D10 OS=Meloidogyne hapla GN=16D10 PE=2 SV=1 MFTNSIKNLIIYLMPLMVTLMLLSVSFVDAGKKPSGPNPGGNN
--help / -h Display help
This flag displays the help.