BnaScope · Help

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).

Accession suffix reference

Accession	Suffix	Accession	Suffix
Westar (WE)	W	ZS11	Z
BH	BH	862(BL)	BL
BU	BU	DaAe	DA
Darmor	D	Express617	Ep617
GH06	GH06	GanganF73	GF73
RB	RB	352(SW)	SW
TA	TA	ZS2	Z2
Zy821	Zy821	no2127	n2127
p130	p130	p202	p202
quintaA	qA	shengli3	sl3
xiaoyun	xy	zheyou7	zy7

Tutorial

Help & Documentation

Welcome to the BnaScope help center. This page provides step-by-step guidance on how to utilize our "gene-centric" database to accelerate your research in Brassica napus.

1. Searching for Genes

BnaScope provides a multi-dimensional search engine to help you find specific genes across 2 reference genomes and 20 genome assemblies.

Global Search: You can retrieve genes by entering a Gene ID (e.g., BnaA01G00010L), Symbol (e.g., FLC), or Keywords.
Functional Retrieval: Search for groups of genes based on Pfam domains, PANTHER gene families, or GO terms.
Location-based Search: Browse specific genomic regions by inputting chromosomal coordinates.

2. Navigating the Unified Gene Reporting Page

Each gene in the database has a standardized reporting page that integrates multiple layers of evidence.

Genomic Attributes: View basic information including genomic location, strand, and sequence.
Functional Predictions: Access deep functional insights, including InterProScan domain results, KEGG pathways, and GO annotations.
Subcellular Insights: Check predicted subcellular localization (DeepLoc 2.1) and signal peptides (SignalP 6.0).
Expression Patterns: For the ZS11 genome, view tissue-specific expression heatmaps derived from 273 RNA-seq datasets.

Figure 1. Components of the BnaScope gene query page. A. Basic gene information, transcript structure, and functional annotations derived from Arabidopsis homologs. B. Sequence information corresponding to the transcript. C. Gene expression profiles across multiple tissues. D. Multiple functional domains annotated by InterProScan, along with subcellular localization and signal peptide predictions from DeepLoc and SignalP. E. Gene Ontology (GO) and KEGG annotations.

3. Using the Homoeolog Viewer

The Homoeolog Viewer is designed to address the complexity of the allotetraploid AACC genome by integrating homoeologous relationships.

Input: Enter a unified Gene Symbol to see all corresponding copies across the A and C subgenomes.
Visualizing Divergence: Use the interactive interface to compare:

Phylogenetic Trees: View the genetic distance between copies.
Gene Structure: Compare exon/intron arrangements side-by-side.
Expression Bias: Analyze heatmaps to identify which homoeolog is dominant in specific tissues.
Multiple Sequence Alignment (MSA): Compare protein sequences and domain distributions powered by MUSCLE v5.

Figure 2. Components of the BnaScope Homoeolog Viewer page. A. Search tool for functional homoeolog clusters, supporting multiple query methods across 22 genome assemblies. B. Basic information of the functional homoeolog cluster and BnaOG assignment. C. Phylogenetic distances and gene structures of homoeologs. D. Functional domain comparison and multiple sequence alignment (MSA) results of homoeologs. E. Expression heatmap of homoeologs.

4. Interactive Genome Browser (JBrowse2)

BnaScope deploys JBrowse2 for an integrated view of structural and functional features.

Structural Tracks: View gene models and over 1 million transposable elements (TEs) annotated via the EDTA pipeline.
Epigenomic Tracks: For ZS11 v1, you can synchronously view ATAC-seq (chromatin accessibility) and ChIP-seq (histone modifications) alongside gene expression signals.
Population Variation: Explore SNP and InDel information derived from 505 resequencing accessions to study natural variations.

Figure 3. JBrowse2 visualization of the ZS11 v1 genome. The view encompasses gene models, TE annotations, variation annotations derived from a population of 505 accessions, multi-tissue RNA-seq expression levels, and epigenetic modification signals including ChIP-seq and ATAC-seq.

5. Online Analysis Toolkits

We provide specialized tools to ensure data compatibility and ease of use:

BLAST+ Server: Perform homology searches against 26 genome versions, including the 22 new assemblies and 4 legacy versions.
ID Conversion: Seamlessly convert between old version IDs and new BnaScope IDs to maintain data continuity across publications.
Flanking Sequence Fetch: Retrieve up- or down-stream sequences for specific genes for primer design or promoter analysis.
Enrichment Analysis: Perform GO and KEGG enrichment for gene lists of interest.

6. User Feedback & Enhancement Program

We are committed to providing an exceptional research experience for the Brassica napus community. To better serve your needs, we cordially invite you to participate in the BnaScope Enhancement Program.

Whether you encounter technical issues or have suggestions for new features, your feedback is vital to our continuous improvement. Currently, we are prioritizing enhancements in two key areas:

Feature Addition: Suggestions for new bioinformatics tools, data types, or analysis functions.
Page Optimization: Improvements to the user interface, visualization clarity, or navigation efficiency.

The BnaScope project team will carefully evaluate every submission and prioritize these updates in our development roadmap.

How to Submit Feedback:

Please record your suggestions in our shared checklist: BnaScope Enhancement Checklist (Public Version)

Note: You are welcome to submit your feedback in either English or Chinese (中文). Thank you for your continued support and contribution to the rapeseed research community!

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.