Universal search: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Search similar protein sequences with remote BLAST

dnakit.databases.blast_protein_search(*, sequence, database=None, expect=None, hitlist_size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
sequence	string	Required	Protein sequence to search (minimum 10 amino acids)
database	string	None	Database to search. Options: 'nr' (comprehensive but slow), 'swissprot' (curated, faster), 'pdb' (protein structures only)
expect	number	None	E-value threshold for reporting hits
hitlist_size	integer	None	Maximum number of hits to return
verbose	bool	True	Progress flag.