BLAST Sequence Search

Pantograph can map query sequences against any set of genomes contained in the pangenome using BLAST. This lets you locate genes, transcripts, primers, or any nucleotide/protein sequence of interest directly on the chromosome-specific graphs and inspect the underlying alignments.

Working with BLAST involves three steps:

1. Run a BLAST pipeline to map your queries against selected genomes.
2. Explore the hits in the Genome View — view hit distribution, filter hits, and inspect alignments.
3. Jump to a hit in the Graph View to browse it in the pangenome context.

Run a BLAST Pipeline

New BLAST searches are started on the Pipeline page under the BLAST Management tab. Click New BLAST Pipeline and fill in the form:

• Pipeline name: a unique name for this search. It will appear in the BLAST selection menu.
• Query sequences: provide your queries in FASTA format by one of three methods — paste the sequence, upload a query file (.fa, .fasta, .fastq, also .gz-compressed), or reference a file already in the bucket by its path.
• Target sequences: select one or more genomes to search against (with Select all / Select none shortcuts).
• Target sequence type: search against genomic sequences, coding sequences (CDS), or protein sequences.
• BLAST method: choose the appropriate program (blastn, blastp, blastx, tblastn, tblastx).
• Maximum e-value: upper bound for reported hits.
• Maximum number of hits per query: how many hits to keep per query.
• Short read mode: enable BLAST settings optimized for short query sequences.
• Notify me: receive an e-mail when the pipeline finishes.

Click Start Pipeline to launch the search. Progress can be followed on the Pipeline Status page.

INFO

Pantograph displays a maximum of 50 hits per query in the interface. Downloadable alignments (from the pipeline results) include all hits.

TIP

The full alignment results as BLAST TSV table and list of alignments can be downloaded from the Browse results action on the Pipeline Status page.

Explore BLAST Hits in the Genome View

After a BLAST pipeline has finished, its hits become available in the Genome View. Open the Tracks Menu ("Data Management") from the Genome Toolbar and switch to the BLAST tab.

Selecting BLAST pipelines

• Search and select one or more BLAST pipelines from the dropdown. Their hits are drawn as colored strips along the chromosomes.
• Each selected pipeline appears as a colored chip. Click a chip to view the pipeline's alignments in the Alignment View.
• Hover a chip to highlight its hits.
• Double-click a chip to keep them highlighted.

INFO

BLAST and QTL selections share a common display limit. A "maximum selection reached" note appears when the combined number of selected traits and pipelines hits the limit.

Coloring hits

Use the Color by dropdown to choose which aggregated statistic determines the color of a hit strip — for example the number of alignments in a bin, or the minimum / mean / maximum e-value, bit score, percent identity, or query coverage. The Genome Legend shows the corresponding light-to-dark color gradient.

Filtering hits

Open Filters to restrict which hits are shown. Each filter can be enabled independently and adjusted with a range slider or by typing exact minimum/maximum values. You can filter hits by e-value, bit score, % identity and query coverage, keeping only those that fall within the range you set. A badge indicates how many filters are currently active.

Alignment view

The Alignment View lists the individual BLAST hits for the selected pipelines (or for a selected region).

Each hit shows the chromosome (for DNA as BLAST target) or transcript (for CDS or protein as target), its genomic coordinates, a color-coded e-value chip, and the pipeline name.

• Hover a hit to highlight its location in the Genome View.
• Expand a hit to load and view its alignment.
• Copy a hit's alignment to the clipboard.
• Open in a bigger window to view the alignment (and filters) in a wider pop-out dialog.

Restricting the alignment view to a region by clicking a BLAST strip on a chromosome. It will filter the alignment view to only the hits within that region.

Navigate to a Hit in the Graph View

From an expanded hit in the alignment view, choose Navigate to hit in graph view. Pantograph switches to the Graph View, centers and zooms on the hit's region, and loads the selected BLAST tracks so you can inspect the hit in its pangenome context. BLAST hits are also loaded as tracks when you open the Graph View of a chromosome for which BLAST pipelines are selected.

Clicking on a BLAST hit band opens the Alignment View that lists all hits overlapping the clicked pangenome column.