SyntenyPair Explorer

Two-genome comparative genomics — zoom, pan, block coloring, gene search, PNG export

Genome 1 FASTA (optional)

Genome 2 FASTA (optional)

BLAST outfmt6 or MCScan colinearity

GFF3 — Genome 1

GFF3 — Genome 2

BLAST tab: query/subject = chromosome names (coords → overlapping genes) or gene IDs (direct match). MCScan: col2 = gene1 ID, col3 = gene2 ID. GFF: gene/mRNA/transcript; ID= attribute matched to synteny file.

— or resume a saved session — 📁 Load Session (.json)

G1 seq:

G2 seq:

G1 region:

G2 region:

Zoom to:

Find gene:

Flank:

(both tracks equal)

Blocks:

🔍 Gene-context zoom Shows 10 flanking genes on each side in both genomes. Partner genome window centred on the syntenic counterpart, extending ±10 genes.

Orient:

Anchor:

Genes:

Show names

+ strand

− strand

Links:

Color by block

≥80%

60–80%

<60%

Opacity100%

Track BG:

Spacing

Scale bar:

Preset:

🎯 Gene Highlights IDs · arrow · body · label · lbl src · ptr color · txt color · angle · ☑ callout · ☑ inside lbl

No entries yet — click + Add to create one.

📊 Assembly & Annotation Summary (requires optional genome FASTA input)

No data loaded yet.

+ strand

− strand

find/hover

link ≥80% id

link 60–80%

link <60%

block-colored