Rnacentral Genome Tools

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

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

Available Tools

RNAcentral_get_genome_locations (Type: RNAcentralGenomeTool)

Get the genomic coordinates of a non-coding RNA in a specific organism from RNAcentral. Provide a…

RNAcentral_get_genome_locations tool specification

Tool Information:

  • Name: RNAcentral_get_genome_locations

  • Type: RNAcentralGenomeTool

  • Description: Get the genomic coordinates of a non-coding RNA in a specific organism from RNAcentral. Provide an RNAcentral URS identifier (e.g. ‘URS00003B7674’ for let-7a) and an NCBI taxonomy id (e.g. 9606 for human). Returns each genomic mapping: chromosome, strand, start, end, UCSC/Ensembl assembly (GRCh38), and GCA accession. RNAcentral aggregates ncRNAs (miRNA, lncRNA, rRNA, snoRNA, tRNA, etc.) from 40+ member databases.

Parameters:

  • operation (string) (optional) Fixed to ‘genome_locations’ for this tool.

  • urs_id (string) (required) RNAcentral URS identifier, e.g. ‘URS00003B7674’. A trailing ‘_taxid’ suffix is accepted and stripped.

  • taxid (integer) (required) NCBI taxonomy id of the organism whose genome mapping is requested, e.g. 9606 (human), 10090 (mouse). Required.

Example Usage:

query = {
    "name": "RNAcentral_get_genome_locations",
    "arguments": {
        "urs_id": "example_value",
        "taxid": 10
    }
}
result = tu.run(query)

RNAcentral_get_sequence (Type: RNAcentralGenomeTool)

Get the nucleotide sequence (FASTA) of a non-coding RNA from RNAcentral. Provide an RNAcentral UR…

RNAcentral_get_sequence tool specification

Tool Information:

  • Name: RNAcentral_get_sequence

  • Type: RNAcentralGenomeTool

  • Description: Get the nucleotide sequence (FASTA) of a non-coding RNA from RNAcentral. Provide an RNAcentral URS identifier (e.g. ‘URS00003B7674’). Returns the FASTA header, the full RNA sequence string, and its length.

Parameters:

  • operation (string) (optional) Fixed to ‘sequence’ for this tool.

  • urs_id (string) (required) RNAcentral URS identifier, e.g. ‘URS00003B7674’. A trailing ‘_taxid’ suffix is accepted and stripped.

Example Usage:

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