Dfam Tools#

Configuration File: dfam_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

Dfam_get_annotations (Type: DfamTool)#

Get transposable element (TE) annotations for a genomic region from Dfam. Returns all TE/repeat e…

Dfam_get_annotations tool specification

Tool Information:

  • Name: Dfam_get_annotations

  • Type: DfamTool

  • Description: Get transposable element (TE) annotations for a genomic region from Dfam. Returns all TE/repeat element hits in the specified chromosomal region including family name, type (SINE, LINE, DNA, LTR, Satellite), strand, bit score, E-value, and alignment coordinates. Useful for analyzing repeat content of a genomic locus, identifying TEs near genes, or studying TE distribution. Example: chr1:10000-50000 in hg38 returns hits including TAR1 satellites, L1MC4a LINEs, MER5B DNA transposons, MIR1 SINEs.

Parameters:

  • assembly (string) (optional) Genome assembly name (default ‘hg38’). Options: ‘hg38’, ‘hg19’, ‘mm10’, ‘mm39’, ‘dm6’, etc.

  • chrom (string) (required) Chromosome name (e.g., ‘chr1’, ‘chr17’, ‘chrX’).

  • start (integer) (required) Start position (0-based).

  • end (integer) (required) End position.

  • nrph (boolean) (optional) Non-redundant profile hits only (default true). Set false for all hits.

Example Usage:

query = {
    "name": "Dfam_get_annotations",
    "arguments": {
        "chrom": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)

Dfam_get_family (Type: DfamTool)#

Get detailed information for a specific Dfam transposable element family by accession. Returns co…

Dfam_get_family tool specification

Tool Information:

  • Name: Dfam_get_family

  • Type: DfamTool

  • Description: Get detailed information for a specific Dfam transposable element family by accession. Returns consensus sequence, taxonomic classification, repeat type/subtype, clade distribution, author, citations, and curation state. Useful for studying TE biology, understanding repeat element structure, or getting consensus sequences for bioinformatics analysis. Example: DF000000003 returns AluSc (309bp SINE/Alu, consensus sequence, found in primates, published Jurka 1988).

Parameters:

  • accession (string) (required) Dfam family accession (e.g., ‘DF000000003’ for AluSc, ‘DF000000053’ for AluYa5).

Example Usage:

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

Dfam_search_families (Type: DfamTool)#

Search Dfam repeat families with explicit offset pagination and pages up to 1000 records. Returns…

Dfam_search_families tool specification

Tool Information:

  • Name: Dfam_search_families

  • Type: DfamTool

  • Description: Search Dfam repeat families with explicit offset pagination and pages up to 1000 records. Returns family accession, classification, length, and repeat type; metadata reports the exact total, truncation, and next_offset.

Parameters:

  • name_prefix (string) (optional) TE family name prefix to search (e.g., ‘AluS’, ‘L1M’, ‘SVA’, ‘MER’). Case-sensitive.

  • clade (string) (optional) Taxonomic clade filter as NCBI taxon ID (e.g., ‘9606’ for human, ‘40674’ for Mammalia, ‘7227’ for Drosophila).

  • repeat_type (string) (optional) Repeat type filter. Options: ‘SINE’, ‘LINE’, ‘LTR’, ‘DNA’, ‘Satellite’, ‘RC’, ‘Other’.

  • limit (integer) (optional) Maximum number of results (default 20, max 1000). Values above 1000 are rejected explicitly.

  • offset (integer) (optional) Zero-based result offset, mapped to Dfam’s official start parameter. Continue with metadata.next_offset.

Example Usage:

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