Blast Tools

Configuration File: blast_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the blast_tools.json configuration file.

Available Tools

BLAST_nucleotide_search (Type: NCBIBlastTool)

Search nucleotide sequences using NCBI BLAST blastn against nucleotide databases. Requires Biopyt…

BLAST_nucleotide_search tool specification

Tool Information:

  • Name: BLAST_nucleotide_search

  • Type: NCBIBlastTool

  • Description: Search nucleotide sequences using NCBI BLAST blastn against nucleotide 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 smaller databases like ‘refseq_select_rna’ instead of ‘nt’.

Parameters:

  • sequence (string) (required) DNA sequence to search (minimum 10 nucleotides)

  • database (string) (optional) Database to search. Options: ‘nt’ (comprehensive but slow), ‘refseq_select_rna’ (curated, faster), ‘refseq_representative_genomes’ (representative genomes)

  • expect (number) (optional) E-value threshold for reporting hits

  • hitlist_size (integer) (optional) Maximum number of hits to return

Example Usage:

query = {
    "name": "BLAST_nucleotide_search",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

BLAST_protein_search (Type: NCBIBlastTool)

Search protein sequences using NCBI BLAST blastp against protein databases. Requires Biopython (p…

BLAST_protein_search tool specification

Tool Information:

  • Name: BLAST_protein_search

  • Type: NCBIBlastTool

  • Description: 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’.

Parameters:

  • sequence (string) (required) Protein sequence to search (minimum 10 amino acids)

  • database (string) (optional) Database to search. Options: ‘nr’ (comprehensive but slow), ‘swissprot’ (curated, faster), ‘pdb’ (protein structures only)

  • expect (number) (optional) E-value threshold for reporting hits

  • hitlist_size (integer) (optional) Maximum number of hits to return

Example Usage:

query = {
    "name": "BLAST_protein_search",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)