Cortexa research tool·genomics·blast

BLAST Protein Search

Search protein sequences using NCBI BLAST blastp against protein databases. Requires Biopython (pip install biopython). IMPORTANT: This tool uses NCBI's remote BLAST service which is inherently SLOW - expect 5-30 minutes per query depending on server load. This is normal NCBI behavior, not a bug. For faster results, use 'swissprot' or 'pdb' databases instead of 'nr'.

SlowCortexa

Status

Succeeds, but routinely takes more than 8 seconds. Hidden from the agent's default toolset; available via opt-in.

Note: BLAST searches typically run 30s–2min upstream; not exposed to anonymous Try-It.

Last probed: never
Last success: never
Last latency: —

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "database": {
      "default": "nr",
      "description": "Database to search. Options: 'nr' (comprehensive but slow), 'swissprot' (curated, faster), 'pdb' (protein structures only)",
      "type": "string"
    },
    "expect": {
      "default": 10,
      "description": "E-value threshold for reporting hits",
      "type": "number"
    },
    "hitlist_size": {
      "default": 50,
      "description": "Maximum number of hits to return",
      "type": "integer"
    },
    "sequence": {
      "description": "Protein sequence to search (minimum 10 amino acids)",
      "type": "string"
    }
  },
  "required": [
    "sequence"
  ],
  "type": "object"
}

Examples (1)

Default BLAST Protein Search call

input

{
  "expect": 1,
  "hitlist_size": 1,
  "sequence": ""
}

Expected response keys: success

Identifiers

Catalog ID: tu_BLAST_protein_search
Tool name: BLAST_protein_search
Added: 2026-04-30 22:47Z
Tags: tooluniverse, slow

BLAST Protein Search

SlowCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "database": { "default": "nr", "description": "Database to search. Options: 'nr' (comprehensive but slow), 'swissprot' (curated, faster), 'pdb' (protein structures only)", "type": "string" }, "expect": { "default": 10, "description": "E-value threshold for reporting hits", "type": "number" }, "hitlist_size": { "default": 50, "description": "Maximum number of hits to return", "type": "integer" }, "sequence": { "description": "Protein sequence to search (minimum 10 amino acids)", "type": "string" } }, "required": [ "sequence" ], "type": "object" }