Ampsphere Record Tools

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

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

Available Tools

AMPSphere_get_amp (Type: AMPSphereGetAmpTool)

Get the full AMPSphere record for one antimicrobial peptide (AMP) by accession. AMPSphere (Big Da…

AMPSphere_get_amp tool specification

Tool Information:

  • Name: AMPSphere_get_amp

  • Type: AMPSphereGetAmpTool

  • Description: Get the full AMPSphere record for one antimicrobial peptide (AMP) by accession. AMPSphere (Big Data Biology Lab) is a global survey of 863,498 AMPs predicted from metagenomes/metaproteomes. Returns the amino-acid sequence, SPHERE family, length, physicochemical properties (molecular_weight, isoelectric_point, charge, aromaticity, instability_index, gravy), quality-control flags (Antifam, RNAcode, metaproteomes, metatranscriptomes, coordinates; each Passed/Failed/Not tested), predicted secondary_structure (helix/turn/sheet fractions), and a metadata.data[] array of gene/sample provenance rows (GMSC gene accession, gene sequence, sample, habitat, microbial source, geography). Keyless public API.

Parameters:

  • accession (string) (required) AMPSphere AMP accession of the form ‘AMP10.XXX_XXX’. Example: ‘AMP10.000_000’ (sequence KKVKSIFKKALAMMGENEVKAWGIGIK, family SPHERE-III.001_493).

Example Usage:

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

AMPSphere_sequence_match (Type: AMPSphereSequenceMatchTool)

Check whether an exact amino-acid sequence already exists in AMPSphere (the global survey of 863,…

AMPSphere_sequence_match tool specification

Tool Information:

  • Name: AMPSphere_sequence_match

  • Type: AMPSphereSequenceMatchTool

  • Description: Check whether an exact amino-acid sequence already exists in AMPSphere (the global survey of 863,498 metagenomic antimicrobial peptides) and, if so, return its AMPSphere accession. This is an exact-match membership test, not a homology search (for homology use AMPSphere’s /search/mmseqs or /search/hmmer endpoints). Returns {query, result, matched}: result is the AMPSphere accession (e.g. ‘AMP10.000_000’) when the sequence is a catalog member, or null when it is not present. The match is case-insensitive here (input is uppercased before querying). Keyless public API.

Parameters:

  • query (string) (required) Amino-acid sequence (single-letter code) to test for exact membership. Example: ‘KKVKSIFKKALAMMGENEVKAWGIGIK’ -> AMP10.000_000.

Example Usage:

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