Uniref Tools#

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

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

Available Tools#

UniRef_get_cluster (Type: UniRefTool)#

Get detailed information about a UniProt UniRef protein sequence cluster. UniRef clusters group r…

UniRef_get_cluster tool specification

Tool Information:

  • Name: UniRef_get_cluster

  • Type: UniRefTool

  • Description: Get detailed information about a UniProt UniRef protein sequence cluster. UniRef clusters group related protein sequences at different identity thresholds: UniRef100 (identical sequences + sub-fragments), UniRef90 (90%+ identity), UniRef50 (50%+ identity). Returns cluster name, member count, representative member details (protein name, organism, accession, sequence length), common taxon, seed sequence, update date, and full protein sequence. Use this to understand protein sequence families and find representative sequences.

Parameters:

  • cluster_id (string) (required) UniRef cluster ID. Format: UniRefNN_ACCESSION. Examples: ‘UniRef90_P04637’ (p53 cluster at 90% identity, 160 members), ‘UniRef50_P04637’ (p53 at 50% identity), ‘UniRef100_P04637’ (identical to p53), ‘UniRef90_P00533’ (EGFR at 90%).

Example Usage:

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

UniRef_search_clusters (Type: UniRefTool)#

Search UniProt UniRef protein sequence clusters with official cursor pagination. Metadata reports…

UniRef_search_clusters tool specification

Tool Information:

  • Name: UniRef_search_clusters

  • Type: UniRefTool

  • Description: Search UniProt UniRef protein sequence clusters with official cursor pagination. Metadata reports the true upstream total and next_cursor; pass that opaque cursor back for the next distinct page.

Parameters:

  • query (string) (required) Search query. Examples: ‘p53’, ‘insulin’, ‘kinase Homo sapiens’, ‘BRCA1’, ‘hemoglobin’. Supports protein names, gene symbols, organism names.

  • cluster_type (string) (optional) Cluster identity level: ‘UniRef100’ (identical), ‘UniRef90’ (90% identity, default), ‘UniRef50’ (50% identity). Invalid values return an error rather than silently removing the identity filter.

  • size (integer) (optional) Results per cursor page (default 10, official API maximum 500). Invalid values return an error rather than being silently clamped.

  • cursor (string) (optional) Opaque cursor from metadata.next_cursor. Omit for the first page.

Example Usage:

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