Dashboard Features

PlasmidNet has 11 interactive tabs providing comprehensive plasmid analytics across 182,362 plasmids (72,556 PLSDB + 109,806 NCBI) with 600,896 AMR annotations.

Overview

Hero banner with total plasmid count, source breakdown (PLSDB + NCBI), and key statistics. Collapsible “About PlasmidNet” section with project motivation.

Charts: topology, source, kingdom distributions, temporal trends (1982-2024), GC content, and plasmid length distributions.

Taxonomy

Top 20 host bacterial genera with interactive search by genus or species. Top genera: Escherichia (14,804), Klebsiella (12,213), Salmonella (3,524), Enterococcus (3,231), Staphylococcus (3,180).

AMR

  • Drug Class Distribution: Top 20 AMR drug classes from the full database

  • Individual Gene Frequency: Top 30 AMR genes coloured by real drug class (sul1, qacEdelta1, blaTEM-1, sul2, tet(A), aph(6)-Id)

Viewer

Interactive circular plasmid map (Plotly Barpolar) for any NCBI accession with zoom and hover tooltips.

Genes auto-classified: AMR (red), MOB (amber), TA (orange), VIR (dark red), QAC (teal), Metal (purple). GC content deviation ring. Works for PLSDB and any NCBI GenBank accession (automatic fallback).

Inc/MOB/IS

Incompatibility Groups & Mobility

  • Top 20 replicon types (IncFIB, IncFII dominant)

  • Predicted mobility: conjugative 31%, mobilizable 29%, non-mobilizable 40%

  • Relaxase types (MOBF, MOBP, MOBQ, MOBH, MOBC, MOBV)

  • MPF types (MPF_F, MPF_T, MPF_I)

IS Elements & Transposon Families (438,616 annotations)

  • IS26 (48,228), IS3 (21,125), IS5 (14,932), IS110 (10,905), Tn3 (9,361)

  • IS families by mobility type

  • IS families by Inc group (heatmap)

Correlations (n = 72,556)

  1. AMR Drug Class vs Inc Groups & Mobility

  2. Heavy Metal Resistance (mercury, arsenic, copper, silver, tellurium)

  3. Phage & Mobile Elements

  4. pMLST Distribution

  5. Virulence Factors (6,145 plasmids)

  6. Toxin-Antitoxin Systems (40,759 plasmids from PGAP)

  7. QAC Resistance (16,948 plasmids)

Geography (57,751 geolocated plasmids)

  1. Global Plasmid Map by mobility (scatter map with hover)

  2. Country Comparison — mobility and Inc distribution by top 20 countries

  3. Temporal Spread Animations — animated timeline 2000-2024 for all plasmids, specific Inc groups, and mobility types (dropdown-driven)

  4. Plasmid Host & Source — Human (11,464), Animal (5,925), Soil (1,576), Water (1,332), Food (1,059), Environment (959). Heatmaps for Inc groups and AMR by host.

Analytics

UMAP Clustering

15,000 plasmids in 2D feature space coloured by mobility and genus. Reveals natural plasmid ecotypes.

Matched Comparison

Conjugative % by species x country. Controls for species composition bias. Key finding: Escherichia in China 54% conjugative vs 35% in Germany.

Rarefaction Analysis

Bootstrap subsampling (50x) to test sample size effects on mobility ratios.

XGBoost + SHAP (82.6% accuracy)

Pre-computed at startup. Feature importance for predicting mobility.

Simpson’s Paradox Detector

Flags Inc groups with species-level trend reversals (>20pp spread).

AMR Co-occurrence Network

Heatmap of resistance genes co-occurring on the same plasmid.

Integron & Gene Cassette Analysis (5,371 plasmids)

Class 1 integrons (qacEdelta1 + sul1). Gene cassettes within 5kb: sul1, aadA2, dfrA12, arr-3, catB3, blaOXA-1. 74% on conjugative plasmids.

Co-mobilization (45% co-location rate)

Conjugative x mobilizable Inc group pairs. Relaxase x T4SS compatibility heatmap. ML predictor (77% accuracy) identifying relaxase type as strongest predictor.

Retro-mobilization & HGT Routes

Transfer mechanisms for 28,816 non-mobilizable plasmids:

  • Retro-mobilization: 9,555 (33%) share host with conjugative plasmid

  • Mobilizable relay: 10,736 (37%)

  • Transduction: 8,585 (30%) small enough for phage capsids

  • 2,226 non-mob with AMR + conjugative partner = retro-mobilization risk

blaKPC Transposon Context (4,800+ plasmids)

Genes within 5kb of blaKPC (blaTEM, blaCTX-M-65, sul1). NTEKPC elements characterised as true transposons. blaKPC by Inc group (IncFIB/FII, IncN) and mobility (59% conjugative).

Integron ML & Transposon-AMR Correlations

ML predicting integron carriage. IS family x AMR drug class co-occurrence heatmap.

Compare

Compare up to 10 plasmids with BLASTn + pyCirclize:

  • Enter NCBI accessions or upload FASTA files

  • CDS gene annotations on circular plot (AMR red, MOB amber)

  • Alignment links colour-coded by identity

  • CDS annotation tables per plasmid

  • Download as FASTA or GenBank format

Seq Analysis

Scan any DNA sequence (NCBI accession, file upload, or paste/edit):

Feature

Method

Restriction sites

25 common enzymes + reverse complements

RE hotspots

500bp windows with 3+ sites

Cryptic promoters

-35 + spacer + -10 (sigma-70)

RBS (Shine-Dalgarno)

AAGGAG, AGGAGG + downstream ATG

Vector signatures

pUC, pBR322, ColE1, T7/T3/SP6, CMV, lacZ, f1

IS elements

IS1, IS26, IS903, IS10, IS3, IS5, ISEcp1, Tn3, Tn21

Direct repeats / TSDs

4-12bp flanking insertions

NTEKPC detection

Tn4401 vs NTEKPC variants around blaKPC

Codon usage bias

Per-window CAI vs E. coli K-12

K-mer naturalness

4-mer entropy + palindrome fraction

Engineering score

0-100 with 5-tier classification

Mobilization assessment

Retro-mobilizable / mobilizable / conjugative

API

Interactive API Explorer tab with dropdown + query input. Also accessible programmatically:

Endpoint

Description

GET /api/

Documentation

GET /api/plasmid/<acc>

Full plasmid details

GET /api/search?q=<query>

Search plasmids

GET /api/amr?gene=<gene>

AMR gene search

GET /api/amr/classes

Drug class counts

GET /api/typing?inc=<inc>

Inc group search

GET /api/typing/mobility

Mobility distribution

GET /api/taxonomy?genus=<genus>

Taxonomy search

GET /api/stats

Database summary