Plasmid Comparison

Compare up to 10 plasmids with BLASTn alignment and pyCirclize circular visualization.

How to Use

  1. Enter accessions (one per line) in the text area:

    MH595534
MH595533
NC_011102.1

  2. Upload FASTA files by dragging & dropping or clicking the upload area

  3. Mix both: Combine accessions with uploaded files (up to 10 total)

  4. Click Compare

Output

Circular Comparison Plot

Generated with pyCirclize:

  • One sector per plasmid with distinct colours

  • Outer ring: CDS genes (blue = CDS forward, green = reverse, red = AMR, amber = MOB)

  • Inner ring: GC content deviation from mean

  • Links between sectors: BLASTn alignment regions, colour-coded by identity

Alignment Table

BLASTn HSPs (High-Scoring Segment Pairs):

  • Query and subject accessions

  • Percent identity

  • Alignment length

  • Query and subject coordinates

CDS Annotation Tables

For each plasmid with GenBank annotations:

  • Gene name, product description

  • Start/end coordinates, strand

Downloads

  • FASTA: Raw sequence for each plasmid

  • GenBank: Annotated GenBank format with CDS features

Requirements

  • BLASTn must be installed for alignment (ncbi-blast+ package)

  • On Heroku, installed via the Aptfile buildpack

  • Locally: brew install blast (macOS) or apt install ncbi-blast+ (Ubuntu)

Example Comparison

Comparing four plasmids from the same study:

MH595534  (9,548 bp, 11 CDS)
MH595533  (14,873 bp, 22 CDS — carries blaKPC-2)
MG786907  (3,812 bp, no annotations)
MH000708  (6,367 bp, no annotations)

The comparison reveals:

  • MH595533 and MH595534 share regions of high identity (>95%)

  • MG786907 and MH000708 lack CDS annotations but their sequences are included in BLASTn

  • Gene names (blaKPC-2, mobA, repA, etc.) are labelled on the outer ring