Tutorial

Overview

A pan-gene groups orthologous genes from many accessions (genomes) into one cluster. PanViewer lets you search by gene ID or keyword, open a pan-gene cluster, choose which accessions and genes to include, and inspect sequence alignment, phylogeny, synteny, expression, and variant summaries in one place.

1. Tabs to select from the available species list. By default, PanViewer opens the Pandagma pan-gene annotations; when additional pan-gene annotations are available (for example PanBARLEX or PanOat), a toggle button under the tabs lets you switch between them.
2. Search bar — input a gene ID or keyword to search. Keywords are matched against gene descriptions of best MMseqs2 hits to Arabidopsis Araport11 and Rice IRGSP-1.0 to identify relevant pan-genes.
3. Saved pan-genes — save pan-gene presets in the browser for easier access on return visits.

Search

Keyword searches first list matching Arabidopsis and rice annotation hits. From there you can narrow results to pan-genes in the active dataset.

1. Select one or more genes from the Arabidopsis or rice gene annotations that appear when a keyword is searched.
2. Press Show pan-genes for selected to show all pan-genes that contain best MMseqs2 hits to the selected genes.
3. Pan-genes are ranked by best e-values to the selected genes. Use the links to open pan-gene pages.

Direct gene-ID searches skip this step and list matching pan-genes immediately. PanViewer may also redirect you to another species tab when a query looks like that species’ gene ID prefix.

Pan-gene page header

The header summarizes the open pan-gene and provides quick exports and preset controls shared across tabs.

1. Pan-gene title.
2. If a reference gene from the pan-gene set is selected, it appears here with available gene descriptions from Arabidopsis and rice based on best MMseqs2 hits.
3. Buttons to download the gene list table, CDS sequences, and protein sequences for the selected genes within the pan-gene.
4. Save pan-gene presets.

Accessions tab

1. Table that allows selection and deselection of specific accessions from the list.
2. Genome assembly versions used for the pan-gene annotation, including links.
3. Count of genes for each genome assembly. For polyploid species, the count is split across sub-genomes.

Genes tab

1. Toggle between different table views and selection options.
2. In the gene view, press gene IDs to select or deselect them. Press the radio button to select a reference gene within the pan-gene to compare to.
3. For polyploids, use the buttons in the headers to select or deselect all homoeologues.
4. Use the buttons next to each gene ID to copy gene IDs, or open windows with additional information such as sequences and links to the GrainGenes BLAST database or genome browsers.

Expression tab

Where expression data are available, PanViewer loads tissue RNA-seq and differential-expression results from PlantApp for reference-genome genes in the cluster.

1. Select from the genes with available gene expression data.
2. Available tissue-specific gene expression and differential expression data (DEG) will appear.
3. Compare the tissue-specific gene expression of up to six genes side by side.

Synteny tab

On coordinate-aware datasets (wheat and oat), synteny draws a neighborhood strip per included focal gene.

1. Select from the options to modify how the synteny plot is generated.
2. Each selected gene in the pan-gene appears as a separate row. Pressing the (−) icon deselects the gene and removes it from the plot.
3. Hover neighboring genes to check for Arabidopsis or rice annotations based on best MMseqs2 hits. Pressing a neighboring gene opens a new tab if that gene is within an annotated pan-gene.

Collinearity tab

Collinearity stacks synteny-style tracks and links genes that share the same pan-gene id across rows.

1. Select from the options to modify how the collinearity plot is generated.
2. Use the buttons next to every gene ID to rotate the orientation, add or remove neighboring genes from the 5′ and 3′ ends, or deselect the gene and remove it from the plot.
3. Hover neighboring genes to check for Arabidopsis or rice annotations based on best MMseqs2 hits. Pressing a neighboring gene opens a new tab if that gene is within an annotated pan-gene.

Alignment tab

1. Select from the options to modify how the alignment plot is generated. Press Re-align to refresh the alignment if necessary.
2. Protein sequence alignments appear here. If a reference gene is selected, secondary structure predictions appear above the sequences.

Tree tab

1. Select from the options to modify how the alignment plot is generated. Press Re-align to refresh the alignment if necessary.
2. Protein sequence alignments appear here. If a reference gene is selected, secondary structure predictions appear above the sequences.
3. Use FastTree from MSA to generate a more accurate tree than the default tree when ready.

Conservation tab

Conservation summaries require a selected reference gene (choose one on the Genes tab).

1. The top part shows sequence conservation compared to a selected reference gene.
2. The bottom part shows predicted secondary structure conservation compared to a reference gene.
3. Hover over a residue to see additional information.

Variants tab

The variants table lists every alignment column where the reference residue differs from at least one other included gene. Rows are active (non-reference) genes; columns are reference amino-acid positions that vary across the cluster. Cells show the alternate residue (color-coded by amino acid); identical residues to the reference are left blank. A summary above the table reports how many variant sites were found and how many genes were compared. Sort columns by alignment position, allele frequency, or diversity, and export the matrix as TSV. A reference gene must be selected on the Genes tab before this tab populates.

Exports & downloads

From the pan-gene header and individual tabs you can download the active gene list (TSV), CDS and protein FASTA, alignment (FASTA), tree (Newick), variant matrix (TSV), collinearity plot (PNG), and expression tables. Export filenames include a .panviewer.YYYYMMDD. stamp so downloads are easy to trace.