How to use piRNAome

piRNAome integrates human and other-species piRNAs from seven source databases with verified genomic coordinates, isoform families, clusters, and SNV annotation. 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
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

·
Quality — database support: HIGH (≥3 source DBs) / MEDIUM (2) / LOW (1).
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Coord status — genome-verification outcome (EXACT, VERIFIED_WITH_SNV, REALIGNED_*, …).
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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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Clusters — known, de novo, 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).
·
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 · Variants · Databases · Loci** tabs below hold the full annotation, SNVs, 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, SNV 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 = verified-with-SNV, 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 independent-DB support. De-novo clusters additionally show a discovery p-value, BH q-value, and tier. 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 known/de-novo clusters and family overlaps.

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: Known clusters (blue), De novo TIER 1 / 2 / 3, per-strand piRNAs (arrows at base zoom), and a Family overlaps track. Overlapping clusters share one slash-separated tooltip.
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.

SNV Explorer

Browse single-nucleotide variants found within piRNAs, cross-referenced to public resources, with an interpretation for each.

1
Core filters: quality (DB support), coordinate status, chromosome, variant type.
2
Evidence & flags: Population/dbSNP, Clinical/ClinVar, Observed in tumour / normal (COSMIC), Candidate RNA editing (REDIportal); plus A/U tail candidate, non-A/U terminal, multi-locus, allele-conflict, novel.
3
Results. Each SNV shows its single-base position, the read-oriented change at its piRNA position, and interpretation badges. A piRNA's SNV carries public-resource characteristics whenever the variant is recorded in dbSNP / ClinVar / COSMIC / REDIportal. Export as TSV.
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.

·
Source databases: piRBase, piRNAdb, NCBI, piRNABank, piRNAQuest, piOxiDB, proTRAC — counts and overlap.
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Totals: piRNAs, isoform families, known + de-novo clusters, family overlaps, and SNVs.

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 + annotation, SNV results — each with size, md5, 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).