BLAST / Sequence Search

Search nucleotide and protein sequences against NCBI BLAST or smarts.bio's internal smarts.Match index. Use the blast_search tool for structured results.

TOOLblast_search

Run BLASTN, BLASTP, BLASTX, or TBLASTN against NCBI databases or your workspace sequences.

Parameter	Type	Description
sequence *	string	Query sequence (FASTA or raw).
program *	string	`blastn`, `blastp`, `blastx`, `tblastn`.
database	string	`nt`, `nr`, `refseq_rna`, or `swissprot` (default: `nt`).
evalue	number	E-value cutoff (default `0.001`).
max_hits	integer	Max results returned (default 10, max 100).
workspace_id	string	Set to save results to your workspace.

from smartsbio import SmartsBio

client = SmartsBio(api_key="sk_live_...")
ws_id = client.workspaces.list()[0].id

result = client.tools.run(
    tool_id="blast_search",
    input={
        "sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY",
        "program": "blastp",
        "database": "swissprot",
        "evalue": 1e-5,
        "max_hits": 10,
        "workspace_id": ws_id,
    },
)
print(f"Query length : {result['query_len']} aa")
print(f"Hits found   : {result['n_hits']}")
for hit in result["hits"][:5]:
    print(f"  {hit['accession']:<12} {hit['description'][:50]:<50}  e={hit['evalue']:.1e}  id={hit['pct_identity']:.1f}%")

BLAST from an uploaded FASTA file

Upload a multi-sequence FASTA file and run batch BLAST, getting back all hits in one call.

from smartsbio import SmartsBio

client = SmartsBio(api_key="sk_live_...")
ws_id = client.workspaces.list()[0].id

# 1. Upload FASTA
fasta = client.files.upload("sequences.fa", workspace_id=ws_id, path="blast/")

# 2. Batch BLAST
result = client.tools.run(
    tool_id="blast_search",
    input={
        "file_path": fasta["key"],   # use file_path instead of sequence
        "program": "blastn",
        "database": "nt",
        "evalue": 0.001,
        "max_hits": 5,
        "workspace_id": ws_id,
        "output_path": "blast/results/",
    },
)

# 3. Download results table
tsv = client.files.download(result["output_path"], workspace_id=ws_id, dest="./blast/")
print(f"Batch BLAST results saved to {tsv}")