Ena Browser Tools

Configuration File: ena_browser_tools.json Tool Type: Local Tools Count: 6

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

Available Tools

ena_get_entry (Type: ENABrowserRESTTool)

Get entry information from ENA by accession number. Supports EMBL/GenBank accessions only (e.g., …

ena_get_entry tool specification

Tool Information:

  • Name: ena_get_entry

  • Type: ENABrowserRESTTool

  • Description: Get entry information from ENA by accession number. Supports EMBL/GenBank accessions only (e.g., U00096, AJ312385, M15390). Does NOT support RefSeq accessions (NC_*, NM_*, NP_* prefixes). Currently extracts metadata from FASTA header. For comprehensive metadata including project, sample, taxon, publications, and sequence length, use ena_get_entry_summary instead. Returns sequence header information with basic metadata.

Parameters:

  • accession (string) (required) EMBL/GenBank accession number. NOT RefSeq (NC_*, NM_*, NP_*). Examples: ‘U00096’, ‘AJ312385’

  • expanded (boolean) (optional) Return expanded metadata (default: false)

Example Usage:

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

ena_get_entry_history (Type: ENABrowserRESTTool)

Get version history for an ENA entry by accession number. Supports EMBL/GenBank accessions only (…

ena_get_entry_history tool specification

Tool Information:

  • Name: ena_get_entry_history

  • Type: ENABrowserRESTTool

  • Description: Get version history for an ENA entry by accession number. Supports EMBL/GenBank accessions only (e.g., U00096, AJ312385, M15390). Does NOT support RefSeq accessions (NC_*, NM_*, NP_* prefixes). Returns all versions of the entry with version numbers, dates, and status information. Each version includes sequence version number, first public date, last updated date, and current status.

Parameters:

  • accession (string) (required) EMBL/GenBank accession number. NOT RefSeq (NC_*, NM_*, NP_*). Examples: ‘U00096’, ‘AJ312385’

Example Usage:

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

ena_get_entry_summary (Type: ENABrowserRESTTool)

Get comprehensive summary information for an ENA entry by accession number. Supports EMBL/GenBank…

ena_get_entry_summary tool specification

Tool Information:

  • Name: ena_get_entry_summary

  • Type: ENABrowserRESTTool

  • Description: Get comprehensive summary information for an ENA entry by accession number. Supports EMBL/GenBank accessions only (e.g., U00096, AJ312385, M15390). Does NOT support RefSeq accessions (NC_*, NM_*, NP_* prefixes). Returns detailed metadata including description, version, project ID, sample ID, molecule type, taxon ID, data type, publication references, sequence length, and status information. This provides more complete metadata than ena_get_entry.

Parameters:

  • accession (string) (required) EMBL/GenBank accession number. NOT RefSeq (NC_*, NM_*, NP_*). Examples: ‘U00096’, ‘AJ312385’, ‘M15390’

Example Usage:

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

ena_get_sequence_embl (Type: ENABrowserRESTTool)

Get nucleotide sequence in EMBL format from ENA by accession number. Supports EMBL/GenBank access…

ena_get_sequence_embl tool specification

Tool Information:

  • Name: ena_get_sequence_embl

  • Type: ENABrowserRESTTool

  • Description: Get nucleotide sequence in EMBL format from ENA by accession number. Supports EMBL/GenBank accessions only (e.g., U00096, AJ312385, M15390). Does NOT support RefSeq accessions (NC_*, NM_*, NP_* prefixes). Returns EMBL-formatted sequence record.

Parameters:

  • accession (string) (required) EMBL/GenBank accession number. NOT RefSeq (NC_*, NM_*, NP_*). Examples: ‘U00096’, ‘AJ312385’, ‘M15390’

Example Usage:

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

ena_get_sequence_fasta (Type: ENABrowserRESTTool)

Get nucleotide sequence in FASTA format from ENA by accession number. Supports EMBL/GenBank acces…

ena_get_sequence_fasta tool specification

Tool Information:

  • Name: ena_get_sequence_fasta

  • Type: ENABrowserRESTTool

  • Description: Get nucleotide sequence in FASTA format from ENA by accession number. Supports EMBL/GenBank accessions only (e.g., U00096, AJ312385, M15390). Does NOT support RefSeq accessions (NC_*, NM_*, NP_* prefixes). Returns sequence with header information.

Parameters:

  • accession (string) (required) EMBL/GenBank accession number. Supported formats: U#####, M#####, AJ######, AL######, CP######, etc. NOT RefSeq (NC_*, NM_*, NP_*). Examples: ‘U00096’, ‘AJ312385’, ‘M15390’

  • download (boolean) (optional) Force download instead of inline display (default: false)

Example Usage:

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

ena_get_sequence_xml (Type: ENABrowserRESTTool)

Get metadata in XML format from ENA for Study, Sample, Run, Experiment, Analysis, or Taxon record…

ena_get_sequence_xml tool specification

Tool Information:

  • Name: ena_get_sequence_xml

  • Type: ENABrowserRESTTool

  • Description: Get metadata in XML format from ENA for Study, Sample, Run, Experiment, Analysis, or Taxon records. XML format is NOT available for sequence records - use ena_get_sequence_fasta or ena_get_sequence_embl for sequence accessions. Supported accession types: Study (ERP*, SRP*, PRJ*), Sample (ERS*, SRS*, SAM*), Run (ERR*, SRR*), Experiment (ERX*, SRX*), Analysis (ERZ*, SRZ*), Taxon IDs. Returns XML-formatted metadata record with submitter-provided information, cross-references, and FTP locations.

Parameters:

  • accession (string) (required) ENA metadata record accession. Supported types: Study (ERP*, SRP*, PRJ*), Sample (ERS*, SRS*, SAM*), Run (ERR*, SRR*), Experiment (ERX*, SRX*), Analysis (ERZ*, SRZ*), Taxon (numeric ID). NOT for sequence accessions (U#####, M#####, etc.). Examples: ‘SAMEA2620084’ (sample), ‘ERX2484999’ (experiment), ‘562’ (taxon)

Example Usage:

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