How to use piRNAome

piRNAome integrates human and other-species piRNAs from seven source databases with verified genomic coordinates, isoform families, clusters, and internal sequence–reference differences. This guide walks through each page and what every panel does.

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Quick start — one search box, many ID types

Type any of these into the search bar and press Search. piRNAome resolves the identifier and opens the matching record (or a result list).

A
piRNA accession or source ID — piRO-hsa-P01780688, piR-hsa-12537, hsa_piR_009086, DQ582314_piR-32426. Common publication spellings such as piR-651 and piRNA-137463 are normalized to their stored source identifiers.
B
Gene / TE / miRNA name — CYP4F29P, THE1B-int, hsa-miR-10b-5p
C
Cluster or family accession — piRO-hsa-C00014446, piRO-hsa-F00884768
D
Raw sequence (≥8 nt) — CAGCCAACAGGTGTAGAG

Search & entry page

Three zones: filter the collection on the left, read the full record in the middle, and compare every isoform of the family on the right.

The filter rail

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Quality — database support: HIGH (≥3 source DBs) / MEDIUM (2) / LOW (1).
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Coordinate status — genome-alignment outcome, including exact match, accepted alignment with an internal difference, coordinate realignment, or no accepted genomic match.
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Chromosome — restrict to one chromosome.
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Contexts — gene_cds/exon/intron, intergenic, lncRNA, miRNA, transposable_element, pseudogene, …
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Variant types — isoform vs. root: root, snv, 5′/3′ ext or trim, and combinations.
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Flags — 1U primary, 10A secondary, ping-pong.
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Cluster intervals — sourced interval, displayed PICB interval (post-PICB accepted-piRNA-locus enrichment FDR ≤0.05), or unassigned.
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Anchor motifs — 1U, 10A, 1U|10A, pyr1, GC_rich, other.
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DB count — ≥2 / ≥3 / ≥4 source databases.
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Sequences — all, or family roots only.
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Databases — a specific source (piRBase, proTRAC, piRNAQuest, NCBI, piRNAdb, piRNABank, piOxiDB).
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TE classes — Repbase class/family of the overlapping TE.
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Free text — TE name, gene, miRNA, or TE-group ID (exact match).

Reading a record

piRNA entry card — The entry header — accession + legacy ID, family size, status badges, the sequence with its 5′ anchor highlighted, and a six-cell summary (locus & coord status · cluster · 5′ anchor · databases · biogenesis · genomic context). Footer links open the locus in UCSC / JBrowse or as JSON. The **Annotation · Sequence differences · Databases · Loci** tabs below hold the genomic annotation, internal sequence–reference differences, source IDs, and every genomic locus (with Gene/TE overlap and UCSC/JBrowse links).

Family alignment & iso-score (right panel)

Aligned isoforms — Every isoform is aligned to the family **root**, coloured by base, with its 5′/3′ trim or extension, internal base-difference count, length, distance to root, TE annotation, and an **iso-score (/9)**. Above the list, isoform-type chips and an iso-score slider filter the family, with a colour legend (green = exact/concordant, blue = accepted with an internal sequence–reference difference, gold = shifted/realigned, red = no genomic match).

Cluster & family pages

Cluster page — Clicking a cluster accession (in a record or in results) opens its page: coordinates & span, piRNA / accepted-loci / seed-eligible counts, and a **characterization** panel — seed density, 1U/10A fraction, strand split, inter-locus gaps, and matches to named source databases. PICB-detected intervals additionally show an accepted-piRNA-locus enrichment FDR from 1,000 matched random placements. The website displays only PICB-detected intervals with FDR ≤0.05. This statistic tests whether a fixed PICB-detected interval contains more accepted piRNA loci than matched random intervals and is used as the website display threshold; it is not PICB's caller-level FDR. The interval coordinates are relocated while preserving chromosome, interval length, and broad accepted-piRNA-locus opportunity; reads are not permuted and PICB is not rerun. Intervals above the threshold remain in the SQLite database. PICB is cited as Konstantinidou et al., *Cell Reports* 2024, 43:114777 (DOI). The two links at the bottom, **Open in JBrowse** and **Open in the built-in genome browser**, jump straight to the cluster's region — the built-in browser also names and highlights the cluster on arrival.

Genome browser

A cluster-oriented browser organised by chromosome. Navigate by coordinates or by piRNA name, and read piRNAs against sourced cluster intervals, PICB-detected intervals with accepted-piRNA-locus enrichment FDR ≤0.05, and adjacent loci assigned to different families.

Genome browser — base level with Find piRNA — Zoomed to a single locus via **Find piRNA**: the searched piRNA (gold label) is highlighted among the per-strand arrows (colour = family; 5′ dot up = + strand, down = −). Type coordinates in the box, or an accession/alias into **Find piRNA**.

1
Pick a chromosome from the ideogram (bar height = piRNA density), then zoom/pan.
2
Two ways to navigate: type coordinates (chr12:9,331,002-9,331,081 or 1.5M), or use Find piRNA — enter an accession/alias and it jumps to that locus and highlights the piRNA.
3
Tracks: sourced cluster intervals, PICB intervals with FDR ≤0.05, per-strand piRNAs, and adjacent accepted loci assigned to different families. These locus pairs are defined by genomic coordinates and are not direct evidence of an RNA precursor junction.
4
Cluster list below the density lists every cluster on the chromosome; the ▶ arrow jumps the view to that cluster's span. Dual JBrowse links open the same region.

Internal sequence–reference differences

Browse internal nucleotide differences between mature piRNA sequences and accepted genomic loci. These records are not automatically interpreted as genomic variants.

Internal sequence–reference difference table — Each row reports the piRNA and locus, genomic position, piRNA-oriented nucleotide change, Q30 read counts, informative depth, number of samples passing the read checks, reproducibility in at least two samples, and named external database matches.

1
Raw-read filters: show records that passed the read checks, the stricter subset supported in at least two samples, or all catalogue differences.
2
External databases: filter matches to dbSNP, ClinVar or COSMIC separately from matches to REDIportal RNA-editing sites.
3
Results. Read counts and q values show what was observed at the assigned locus. Database matches provide a separate annotation and do not by themselves validate the difference.
4
Back to the record. Click any piRNA to return to the full search / entry page.

Database stats

A one-page overview of what's inside — totals and the contribution of each source database.

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Source databases: piRBase, piRNAdb, NCBI, piRNABank, piRNAQuest, piOxiDB, proTRAC — counts and overlap.
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Totals: piRNA sequences, piRNA families containing at least two members, sourced cluster intervals, PICB intervals with FDR ≤0.05, adjacent loci assigned to different families, and internal sequence–reference differences. Singleton sequences are reported separately and are not counted as families.

Downloads & API

Every dataset as a flat file, plus a no-authentication REST API.

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Data files: piRNA FASTA, genomic GTF, cluster GTF, ID aliases, families, genomic annotation and sequence–reference difference results — each with size, checksum and record count.
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Other species: C. elegans, D. melanogaster, M. musculus, R. norvegicus at species.pirnaome.org; per-species CHECKSUMS.
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REST API: /api/entry/{id}, /api/search, /api/cluster/{id}, /api/snv/search, … (JSON, no auth).