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Comparative Gene Viewer

Explore, compare, and analyze gene structures across species in one unified workspace.
Built for researchers. |

How it works

A simple workflow from gene search to publication-ready results.

1
Choose organism & genome
2
Search genes by name or ID
3
Visualize & compare structures
4
Analyze with interactive charts
5
Export & share results

Core capabilities

Everything you need for comparative gene structure analysis in one place.

Gene search across organisms

Query multiple annotated genes within one organism or compare one gene across species.

Comparative aligned view

Compare representative gene models and label exon-level event patterns across organisms.

Interactive gene cards

Inspect gene structure, transcripts, genomic context, tooltips, zoom, and linked resources.

Built-in analytics

Structural and sequence analytics with 9 chart types — all without leaving the app.

Preloaded & custom data

Work with preloaded references or upload your own genome and annotation pair.

Export & session reuse

Export figures, tables, sequences. Save or restore full sessions for later.

Why CGV was built

Comparative gene structure analysis made easier to inspect, explain, and share — without jumping between browsers, scripts, and static plots.

The problem

Genome browsers are great for locus inspection, but not for clear side-by-side gene structure comparison across species.

The workflow gap

Search, alignment, inspection, and export are usually spread across several tools. CGV unifies them.

Who CGV is for

Biologists, bioinformaticians, and students who want a guided visual workflow instead of code-heavy pipelines.

Scope

CGV is focused on gene-centered structure interpretation. Clear scope helps pair CGV with the right upstream or downstream tools.

Designed for

  • Comparative gene and exon structure analysis across multiple organisms
  • Aligned exon-level relationships in a cross-species context
  • Interactive gene metrics, transcript structure, sequence composition
  • Preloaded references with custom genome and annotation uploads
  • Publication-ready exports: plots, tables, and sequences
  • Session save and restore for reproducible review

Not designed for

  • Differential expression, isoform switching, or abundance testing
  • Variant calling, SNP/INDEL analysis, RNA-seq quantification
  • Whole-genome browsing or large region navigation
  • De novo genome or transcriptome assembly
  • Phylogenetic inference or protein 3D structure prediction
  • High-throughput genome-wide batch analysis

How CGV compares

Compact scope summary:   ✓ native support    ~ possible with limits    ✗ not the main purpose

Capability CGV Ensembl / UCSC JBrowse2 / Apollo IsoformSwitchAnalyzeR / FLAIR gggenomes / gggenes
Cross-species gene structure comparison ✓ ~ locus browsing ~ manual setup ✗ ~ static plots
Representative exon alignment with event labels ✓ ✗ ✗ ✗ ✗
Interactive gene cards plus analytics ✓ ~ limited metrics ~ browser focus ~ analysis focus ~ plot focus
Browser-based workflow, no code required ✓ ✓ ~ config driven ✗ ✗
Custom genome plus annotation uploads ✓ ✗ ✓ ~ ✓
Export figures, tables, sequences, sessions ✓ ~ basic export ~ ~ ~ mostly plots

Scope summary, not benchmark. Many of these tools are complementary and can be combined in one analysis workflow.

Settings

Appearance

Day / Night Mode Switch between the light and dark theme.
Colorblind Palette Enables an accessible color scheme for color vision deficiency.

Interface

Confirm before deleting Show a confirmation dialog before removing plots or sessions.

External alias lookup

Choose which external databases are used when a gene is not found in the local annotation.

Work sessions

Download your current work session (plots and settings) as an .rds file, or upload a previously saved session file to restore it.

Export current session (.rds)

Loading a session replaces current visualizations.

User Guide

CGV User Guide

Everything you need to move from query setup to interpretation. Covers search modes, alignment views, analytics, exports, and troubleshooting.

2 Search modes
5 Visualization views
10 Analytics charts
3 Alignment modes
5+ Export formats
Quick Start

Quick Start Workflow

A practical order for most analyses: pick the right search mode first, then build organisms and gene queries, generate the view, and explore results.

1

Pick a search mode

Choose Multi-Gene Search to compare several genes in one organism, or Cross-Species Gene Search to trace one gene across multiple species.

2

Select organisms

Pick from the preloaded reference genomes or upload your own genome + annotation pair. You can mix preloaded and custom organisms.

3

Enter gene names

Type gene identifiers in the search box. CGV resolves aliases automatically via MyGene, NCBI, UniProt, and Ensembl. In Multi-Gene mode, add all genes before running.

4

Generate the view

Run the visualization. Gene cards load with structure plots, transcript metrics, and quick-action links. Summary table and analytics become available immediately.

5

Explore and export

Use the Summary Table, open the 10 analytics chart panels, click genes for popups (metrics, GO terms, papers, promoter), and export SVG, CSV, FASTA, or a full session.

Search Modes

Search Modes

Two complementary modes. Both share the same interface but unlock different views and comparison frameworks.

Multi-Gene Search

Inspect and compare multiple annotated genes within one organism side by side. Ideal for structural review across isoforms and paralogs.

  • Compare gene architecture, exon/intron metrics, and sequence composition for multiple genes at once.
  • Examine all transcript isoforms per gene with individual structure plots.
  • Access all 10 analytics chart types. Visualize available in: Compact and Detailed views.

Cross-Species Gene Search

Compare one gene across multiple organisms with representative models aligned side by side. Designed for cross-species structural analysis.

  • One gene queried simultaneously in each selected organism.
  • Unlocks the Comparative Aligned View, LASTZ Blocks, and Multi-PIP in addition to Compact and Detailed.
  • Exon-level event labeling: conservation, duplication (1:n, n:1), loss, and partial matches.
Visualization Views

Visualization Views

CGV offers five view modes. Compact and Detailed are available in both search modes. The three alignment views are exclusive to Cross-Species search.

Compact

Minimalist gene structure panel. Fits many genes on screen. Ideal for first-pass inspection.

Both modes

Detailed

Full annotation with exons, CDS, UTR, strand, coordinates and zoom. Best for thorough single-gene review.

Both modes

Comparative Aligned

Selects one representative transcript per organism, aligns them, and displays exon correspondence as ribbons with event-type labels.

Cross-species only

LASTZ Blocks

Local pairwise alignment blocks across the genomic locus showing conserved regions between the query and each reference species.

Cross-species only

Multi-PIP

Percent Identity Plot across the genomic window. Visualizes conservation patterns of the query locus against multiple references.

Cross-species only
Alignment Modes

Alignment Modes (Comparative Aligned View)

The Comparative Aligned View supports three alignment strategies. Each uses a different sequence representation and scoring matrix.

Translated CDS

Aligns the protein translations of each representative CDS. Best for detecting conserved coding regions even across divergent genomes.

BLOSUM62
CDS Nucleotide

Aligns the nucleotide CDS sequences directly. Useful when comparing closely related species where nucleotide identity is high.

EDNAFULL
Exon

Aligns full exon sequences including UTRs. Captures structural variation beyond the CDS and is suitable for lncRNA comparisons.

EDNAFULL

All three modes use Needleman-Wunsch global alignment. Configurable window sizes: gene body, ±5 kb, ±10 kb, ±25 kb, ±50 kb apply to LASTZ Blocks and Multi-PIP.

Results

Understanding Results

CGV returns multiple output layers. Each adds a different level of depth to your analysis.

Gene cards

  • One card per gene with structure plot (exons, CDS, UTR, strand, zoom, hoverable coordinates).
  • Metrics: transcript length, CDS length, protein length (aa), GC%, exon/intron counts, biotype.
  • Quick-action links for alias resolution and direct sequence actions.

Gene card popups

  • Metrics popup — nucleotide composition donut, isoform comparison chart, genomic context scatter.
  • GO Annotations — Gene Ontology terms from local files or live Ensembl lookup.
  • Papers — recent publications via Europe PMC.
  • Promoter — upstream region FASTA (100–5,000 bp) with coordinate export.

Summary Table

  • Sortable and filterable. Columns: gene, transcript, chromosome, strand, exon count, lengths, organism (cross-species mode).
  • Filter or rank results quickly before opening chart panels.
  • Export as CSV for downstream analysis.

10 analytics chart types:

Architecture
Exons & Introns
Sequence
Genomic Context
Exon Lengths
Scatter
Heatmap
Radar
Correlations
Transcript Isoforms
Organisms

Preloaded Reference Genomes

CGV ships with reference genome assemblies and NCBI RefSeq annotations covering three kingdoms. You can also upload custom genomes.

Animalia (11) H. sapiens, M. musculus, P. troglodytes, S. scrofa, C. lupus, D. rerio, X. laevis, D. melanogaster, C. elegans, D. rotundus, E. caballus
Plantae (11) A. thaliana, A. lyrata, Z. mays (2 assemblies), O. sativa (2), S. lycopersicum, S. tuberosum, S. pennellii, H. vulgare, P. vulgaris, T. aestivum
Fungi (4) S. cerevisiae, S. pombe, N. crassa, C. albicans

Upload your own genome

Provide a genome file ( .fa , .fa.gz , .fna , .2bit ) and a matching annotation ( .gff3 , .gtf ). You can mix uploaded and preloaded organisms in the same analysis.

Exports & Sessions

Export Formats & Session Management

Multiple output options for publications, data pipelines, and workspace persistence.

SVG Individual chart or gene structure vector export
ZIP — charts Batch export all analytics panels as SVGs
ZIP — structures Batch export all gene structure plots as SVGs
CSV Summary table: lengths, exon/intron counts, GC%, coordinates
FASTA — promoter Configurable upstream region (100–5,000 bp)
Session (.rds) Save and restore the full workspace from Settings
Troubleshooting

Troubleshooting & Tips

Most issues come from query spelling, organism selection, or annotation structure. This section covers the most common checks.

Data inputs

  • Uploads require a genome file in .fa , .fa.gz , or .2bit plus a matching annotation in .gff3 or .gtf .
  • You can mix preloaded references with uploaded organisms in the same analysis.
  • CGV currently ships with more than two dozen preloaded organism references.

If a gene is missing

  • Check gene symbol spelling and letter case.
  • Confirm that at least one organism is selected before running the search.
  • For uploaded data, verify that the annotation contains the expected gene identifiers and associated transcript features.
MyGene MyGene
NCBI Gene NCBI Gene
UniProt UniProt
Ensembl Ensembl

Performance tips

  • Start with fewer organisms or genes, then scale up once the first view looks correct.
  • Use the summary table to narrow what you inspect before opening all analytics panels.
  • Reorder charts when the plot count grows so comparisons stay readable.

Sessions and display settings

  • Export your current work session as .rds when you want to resume later.
  • Restore a saved session from Settings to recover plots and configuration.
  • Theme, dark mode, and colorblind options can help readability for dense figure review.
FAQ

Frequently Asked Questions

CGV is designed for gene-centered structural comparison. It excels at examining exon/intron architecture, comparing representative gene models across species, exploring transcript isoforms, and producing publication-ready figures — all within a single guided interface, without requiring any scripting.

No. CGV runs entirely in the browser. There is no local installation, package setup, or command-line workflow required to start exploring results.

Multi-Gene Search is the better choice when you want to inspect several genes within one organism. Cross-Species Gene Search is the better choice when you want to compare one gene across multiple organisms and use the Comparative Aligned view.

It selects one representative transcript per organism and aligns them globally using Needleman-Wunsch. The result is displayed as aligned exon blocks connected by ribbons, with each exon-pair labeled by event type:

  • 1:1 — single conserved exon correspondence.
  • 1:n / n:1 — exon split or fusion events.
  • Partial — partial overlap between exons.
  • Lost — exon present in one organism, absent in the other.
  • Translated CDS (BLOSUM62) — recommended for distantly related species where nucleotide identity is low but protein function is conserved.
  • CDS Nucleotide (EDNAFULL) — best for closely related species where the coding sequence at nucleotide level is still similar.
  • Exon (EDNAFULL) — aligns the full exon including UTR regions. Useful for lncRNAs or when UTR conservation is of interest.

Clicking a gene opens a set of popup panels:

  • Metrics — nucleotide composition donut, isoform length comparison, and genomic context scatter.
  • GO Annotations — Gene Ontology terms sourced from local annotation files, with live fallback to Ensembl.
  • Papers — recent publications retrieved from Europe PMC for that gene and organism.
  • Promoter — configurable upstream region (100–5,000 bp) shown as FASTA sequence with coordinate export.

Genome formats: .fa , .fasta , .fna (plain or gzip-compressed), or .2bit .

Annotation formats: .gff3 or .gtf .

The genome and annotation files must correspond to the same organism. You can mix uploaded organisms with preloaded references in the same analysis session.

  • SVG — individual chart or gene structure plot export.
  • ZIP — batch export of all analytics chart SVGs, or all gene structure SVGs.
  • CSV — summary table with lengths, exon/intron counts, GC%, and coordinates.
  • FASTA — promoter region sequences with configurable window (100–5,000 bp).
  • Session (.rds) — saves the full workspace. Restore it any time from Settings → Session Management.
  • The gene symbol may be misspelled or use an alternative alias not present in the selected annotation.
  • No organism is selected for the current search — at least one must be active.
  • For uploaded data, the annotation file may not contain the expected gene identifier or a matching transcript feature.

Tip: enable external alias lookup (MyGene, NCBI Gene, UniProt, or Ensembl) in Settings to automatically resolve alternative names and IDs.

Genome browsers are built for locus navigation and broad genomic context. Plotting packages require scripted figure generation. CGV occupies a different space: guided, gene-first comparison with cross-species alignment, 10 analytics charts, popup information layers (GO, papers, promoter), and multiple export formats — all without writing code.

CGV is focused on gene structure visualization and comparative analysis. It does not perform: RNA-seq quantification, differential expression testing, variant calling, genome assembly, phylogenetic tree construction, or protein structure prediction. For those workflows, use dedicated tools and bring the results back to CGV for structural context.

Search gene
No batch genes.
Visualization mode
Multi-Gene mode
Plot zoom
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