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### Rfam Family (`rfam-family`) Retrieves a family by accession or family ID and returns its description, RNA type, curation information, sequence and species counts, clan membership when available, and the gathering cutoff for family membership. The output also contains the consensus secondary structure, reference annotation, and database release information. The complete Stockholm seed alignment can be included through configuration. #### API Reference

Source Rfam accession (e.g. 'RF01731') or family ID (e.g. 'TwoAYGGAY').

Source Return the full Stockholm seed alignment, not only its consensus lines. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Rfam accession. Rfam family ID. One-line family description. Rfam type annotation (e.g. 'Cis-reg', 'Gene; snRNA'). Curator comment, when the family has one. Family authors. Where the seed alignment came from. Where the consensus structure came from. Sequences in the seed alignment. Annotated regions across all sequences. Species with at least one annotated region. Accession of the clan the family belongs to. ID of the clan the family belongs to. Bit-score threshold for family membership. Rfam release the record comes from. Consensus secondary structure (#=GC SS\_cons), WUSS notation. Reference consensus sequence (#=GC RF), aligned with it. Full Stockholm seed alignment, when requested.

#### Applications Family records provide context for interpreting RNA annotations. The consensus structure describes conserved pairing patterns across the alignment, while the curation fields identify the sources of the alignment and structure. These records support comparisons of representative family sequences and interpretation of model scores alongside the reported cutoffs. The seed alignment can also be used for further alignment or structural analysis. #### Usage Tips * **Families can be identified by accession or ID.** For example, `RF01731` and `TwoAYGGAY` identify the same [Rfam family](https://rfam.org/family/RF01731). The output reports both identifiers. * **Consensus annotations use alignment coordinates.** `consensus_structure` contains the Stockholm `SS_cons` annotation in [WUSS notation](https://docs.rfam.org/en/latest/glossary.html#wuss-format); `consensus_sequence` contains the `RF` reference annotation. These strings include alignment columns and should not be interpreted as an unaligned nucleotide sequence or genomic coordinates. * **Structural annotations have different sources.** Rfam includes both experimentally supported and computationally predicted structures. The `structure_source` field records provenance when available; the [Rfam documentation](https://docs.rfam.org/en/latest/building-families.html) explains why an underlying publication may be needed to establish the type of evidence. * **The seed alignment is optional in the output.** Set `include_seed_alignment=True` to retain it and enable `sto` export. The tool downloads the alignment to extract the consensus annotations even when this option is disabled. Family records can also be exported as JSON.

### Rfam Regions (`rfam-regions`) Retrieves the annotated sequence regions for a family, with optional filters for NCBI taxonomy ID, species name, or sequence accession. Each region contains a versioned sequence accession, Infernal bit score, start and end coordinates, strand, sequence description, species name, and taxonomy ID. The output includes the family identifiers, total and filtered region counts, and a flag indicating whether the returned list was truncated. #### API Reference

Source Keep only hits in this NCBI taxonomy ID. Keep only hits whose species contains this text (case-insensitive). Keep only hits on this sequence accession. The version suffix is optional ('AM181176' matches 'AM181176.4'). Rfam accession (e.g. 'RF01731') or family ID (e.g. 'TwoAYGGAY').

Source Most regions returned after filtering; the rest are counted, not listed. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Rfam accession of the family. Rfam family ID. Rfam release the regions were built from. Regions the family has across all sequences. Regions left after the input filters. Whether matched regions exceeded max\_regions. Matched regions, at most max\_regions of them. Versioned accession of the sequence holding the hit. Infernal bit score of the hit. First position of the hit (1-indexed, inclusive, start \<= end). Last position of the hit (1-indexed, inclusive). Strand of the hit on the sequence. Description of the sequence holding the hit. Species name of the sequence. NCBI taxonomy ID of the species.

#### Applications Region records locate candidate family members in the sequences represented by Rfam. Filtering by species or sequence accession supports examination of annotated loci in a particular organism or genome record. The accession, coordinates, and strand can be passed to [`ncbi-efetch`](https://bio-pro.mintlify.app/tools/database-retrieval/ncbi) to retrieve the corresponding nucleotide subsequence for comparative analysis. Taxonomic fields also support examination of a family's distribution within the Rfam dataset. #### Usage Tips * **Coordinates are 1-indexed and inclusive.** The tool normalizes each region to `start <= end` and reports orientation separately as `+` or `-`. These values correspond to `ncbi-efetch`'s `seq_start`, `seq_stop`, and `strand` inputs. * **Filters are applied after download.** `taxid` matches an exact taxonomy ID, `species` matches a case-insensitive substring, and `sequence_accession` accepts either a versioned or an unversioned accession. When several filters are provided, a region must satisfy all of them. * **The return limit applies after filtering.** `max_regions` defaults to 500. `total_regions` reports the family-wide count, `matched_regions` counts all regions satisfying the filters, and `truncated` indicates that some matching regions were omitted. The limit does not reduce the size of the download. * **Some families are too large for the endpoint.** The [Rfam API documentation](https://docs.rfam.org/en/latest/api.html#sequence-regions) states that the server can refuse region downloads for very large families. Local filters cannot bypass this restriction. * **Region tables can be exported.** JSON preserves the full output, including counts and release information; TSV and CSV contain the returned region rows.