Blast NCBI download

This protocol access the NCBI API using the Entrez module of the Biopython package. The protocol is prepared to fetch protein or nucleotide sequences from the NCBI databases and small molecules from PubChem.

The user can perform a search using NCBI IDs, where the specific objects they refer will be directly fetched; or a broader search using keywords which will return a set of objects which are returned by the esearch functionality. The user must be aware of this functionality, since the outputs might not be those expected.

Input

Note

All parameters include a help button that gives further information for each of them.

Blast NCBI download form

The result of this protocol is either a SetOfSequences (for protein or nucletides sequences) or a SetOfSmallMolecules for PubChem downloads.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests blast.tests.test_blast.TestNCBIDownload