K miR

K-miR: miRNA family annotation from 7-mer seeds

Documentation · Module parameters · CDR1as example

AnnotateMiRNASeeds merges RNA sequence signatures with family seed annotations. It reports candidate seed-compatible miRNAs, not a new miRNA-binding probability or a family-level enrichment test.

Orientation and site definition

The supplied Seed+m8 is positions 2-8 of the mature miRNA. All 2,606 human rows were checked against their mature sequences. TargetScan defines families using these positions.

To match a transcript-oriented query word, reverse complement the seed. Example: miR-7-5p seed GGAAGAC gives target GUCUUCC in RNA, or GTCTTCC in DNA.

This module annotates exact 7mer-m8 sites only. It does not include wobble, mismatches, 6mer, 7mer-A1, 8mer/context classification, accessibility, conservation scoring or miRNA expression. An 8mer includes a matching 7mer-m8 segment, but this join does not classify it as an 8mer. See TargetScan site definitions.

Parameters

AnnotateMiRNASeeds(self, kmers=None, source="KEA",
    reference=None, species=None, species_id=9606,
    plot=True, top_n=20, output_dir=None)

Parameter	Behavior
analysis.seed_family_file	Path to the tab-separated family table. Defaults to the complete table installed with K-tools; set this attribute to use a custom file. Required columns: miR family, Seed+m8, Species ID, MiRBase ID. If Mature sequence is present, positions 2–8 are validated.
species_id	Taxonomy ID for row filtering, default human 9606. The bundled human subset cannot annotate other species.
source	KEA: score join from stored delta-median and stat_log2fc tables; KRS: score join from stored KRS target results; manual: sequence annotation without analysis scores.
kmers	Explicit canonical 7-mers. If omitted in KEA, use the intersection of enriched delta-median and stat_log2fc lists. If omitted in KRS, use the stored selected signature. Required for manual mode. DNA/RNA alphabets are accepted and normalized to DNA. Empty signatures return empty matches. Other lengths raise an error rather than silently decomposing or transferring parent scores.
reference	Optional validation of the stored KRS target ID. To analyze another target, rerun KRS first.
species	Count/results key, default input; distinct from taxonomy species_id.
plot	Draw/save scored annotation plots, default True. Manual mode has no analysis scores and does not plot.
top_n	Positive integer, default 20; limit plotted matched word/family rows, not returned annotations. KEA sorts by log2FoldChange; KRS by target percentile.
output_dir	New output directory; None creates a unique MiRNASeeds_* subdirectory of the analysis output. Existing directories are refused.

Analysis scores and interpretation

KEA has an integrated selection but no defined scalar combined score. The method retains both delta_median and log2FoldChange and plots them in separate panels for matched words from the integrated signature. Original PValue, FDR and bonf are retained when available. They are k-mer test values, not new miRNA-family P values.

KRS retains target_frequency, target_rank_percentile and selected_KRS. The plot shows target percentile, not a calibrated P value or fold enrichment.

Family rows sharing a target word are preserved. Multiple mature miRNAs within a family/seed are grouped into semicolon-separated IDs/accessions. This prevents treating each mature ID as an independent discovered site; family annotations sharing a word still share the same evidence. Plots label each family and word explicitly and do not sum scores across miRNAs.

Unmatched words remain in query_kmers.tsv; the annotation does not discard them silently. Supplied explicit words may be outside the selected signature; their scores are joined where available, and missing score values remain missing.

Launch examples

The bundled table is selected automatically. To use another table, set analysis.seed_family_file = "path/to/miR_Family_Info.txt" before calling the method.

# After k=7 counting and both KEA extraction branches:
mirna = analysis.AnnotateMiRNASeeds(
    kmers=signature,
    source="KEA",
    plot=True,
)

# After KRS(reference="my_target", ...):
mirna = analysis.AnnotateMiRNASeeds(
    source="KRS",
    reference="my_target",
    plot=True,
)

# Orientation check, independent of any analysis:
mirna = analysis.AnnotateMiRNASeeds(
    kmers=["GTCTTCC"], source="manual", plot=False,
)
print(mirna["matches"])

Outputs

Returns matches, query, seed_map, figures, settings, output_dir; also stores analysis.mirna_seed_annotation.

• seed_matches.tsv: matched words, family/seed, mature miRNA IDs and original scores.
• query_kmers.tsv: all unique supplied words and matched-family count.
• family_seed_map.tsv: filtered family-to-target-word mapping.
• settings.json: inputs, site type, selected words and parameters.
• seed_scores.png / seed_scores.pdf when scored matches are plotted.

Figure objects remain available for the caller to display or close. No extra runtime dependencies are needed.