RGMI BnaScope
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Help & Support

BnaScope integrates 22 Brassica napus assemblies (~2.1M genes, 3.4M transcripts) and provides gene search, homoeolog families, expression profiles, JBrowse2 visualization, BLAST/enrichment tools, and unified downloads.

Highlight

  • Data NotesData status, annotation methods, and sources.
  • Gene Naming RulesStandardized chromosome and gene ID conventions.
  • TutorialStepwise guidance with images and rich text.
  • Troubleshooting & FAQAdmin-editable guidance for common issues.

Module Guide

Gene Search & Detail

  • Filter by species, gene ID, symbol, annotation (Pfam/PANTHER/GO/KEGG), or genomic location.
  • Export filtered results to CSV or download sequences for curated gene sets.
  • Gene detail pages summarize protein features, domains, GO/KEGG, homoeologs, and gene structure.

Homoeolog & Gene Family

  • Families are grouped by symbol to compare members and distributions across cultivars.
  • Explore transcription factor families and functional domains to highlight enriched groups.
  • Copies View summarizes homoeolog counts and provides aligned sequence/annotation context.

Omics & Visualization

  • JBrowse2 pan-genome tracks let you inspect genes, variation, and annotations.
  • Expression heatmaps support curated panels and user-provided gene lists.
  • Protein views summarize InterPro/SignalP/DeepLoc features for rapid inspection.

Online Tools

  • BLAST supports genome/CDS/protein searches with FASTA input or file upload.
  • GO/KEGG enrichment accepts gene lists for functional profiling.
  • ID conversion translates between legacy identifiers and standardized Bna IDs.

Downloads & Exports

  • Download curated genome, annotation, CDS, cDNA, and protein files by cultivar.
  • Exports are optimized for large gene sets to keep browser performance stable.
  • Use standardized IDs to keep cross-module results consistent.

Gene Naming Rules

Gene IDs

  • Regular chromosomes: Bna[Chr]G[Number][Suffix], numbering starts at 000010 and increments by 10.
  • Unanchored scaffolds: BnaUanG[Number][Suffix], global counter across all irregular scaffolds in natural-sort order.
  • Examples: BnaA01G000010Z (regular), BnaUanG000010Z (unanchored).

Chromosome naming

  • Regular chromosomes use [Species]_[Chr] where [Chr] is A01–A10 or C01–C09 (e.g., ZS11_A01).
  • Irregular scaffolds use [Species]_[Abbrev][Number][Suffix] with ptg retained and scaffold abbreviated to scd.
  • Leading zeros are removed from numeric parts; existing separators are preserved (e.g., Darmor_scd_38).

Species suffix reference

Species Suffix Species Suffix
Westar (WE) W ZS11 Z
BH BH BL BL
BU BU DaAe DA
Darmor D Express617 Ep617
GH06 GH06 GanganF73 GF73
RB RB SW SW
TA TA ZS2 Z2
Zy821 Zy821 no2127 n2127
p130 p130 p202 p202
quintaA qA shengli3 sl3
xiaoyun xy zheyou7 zy7

Tutorial

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Troubleshooting & FAQ

No results in Gene Search?

Confirm the species is correct and the gene ID/symbol case matches the dataset; relax Pfam/GO filters if results are too narrow.

  • Verify results in the list view before exporting.

BLAST fails or returns empty?

Check FASTA formatting, select the correct target database (genomic/CDS/protein), and keep max_target_seqs ≤ 10000.

  • Shorter sequences and fewer targets often improve responsiveness.

Downloads or exports fail?

Check browser download permissions or try a different browser; for large exports, split gene lists into smaller batches.

  • Return to the Downloads page to restart a controlled download.

Expression or visualization not loading?

Refresh the page, check your network connection, and try a smaller gene list for heavy tracks or heatmaps.

  • JBrowse2 tracks may take longer for dense regions; allow extra time to render.