5. Nucleotide Links

DNA-level synteny showing aligned genomic regions. Nucleotide links represent conserved DNA blocks between genomes, useful for visualizing large-scale rearrangements and syntenic regions.

Data

Nucleotide Links


const nucleotideLinks = [
  // E. coli K-12 vs O157 - very high synteny (same species)
  { seqidA: 'ECO_K12', startA: 500, endA: 9500, 
    seqidB: 'ECO_O157', startB: 600, endB: 9600, similarity: 96.5 },
  { seqidA: 'ECO_K12', startA: 10700, endA: 26000, 
    seqidB: 'ECO_O157', startB: 9300, endB: 25000, similarity: 95.8 },
  
  // E. coli vs Salmonella - high synteny (same family)
  { seqidA: 'ECO_K12', startA: 2700, endA: 9000, 
    seqidB: 'SEN_LT2', startB: 2700, endB: 8950, similarity: 88.2 },
  { seqidA: 'ECO_K12', startA: 10700, endA: 22200, 
    seqidB: 'SEN_LT2', startB: 10300, endB: 21800, similarity: 87.5 },
  
  // Salmonella LT2 vs Typhi - very high synteny (same species)
  { seqidA: 'SEN_LT2', startA: 400, endA: 8950, 
    seqidB: 'SEN_Typ', startB: 550, endB: 8250, similarity: 94.8 },
  { seqidA: 'SEN_LT2', startA: 10300, endA: 25400, 
    seqidB: 'SEN_Typ', startB: 8400, endB: 23500, similarity: 93.5 },
  
  // Klebsiella MGH vs HS11 - high synteny (same species)
  { seqidA: 'KPN_MGH', startA: 300, endA: 13200, 
    seqidB: 'KPN_HS11', startB: 450, endB: 10650, similarity: 94.2 },
  { seqidA: 'KPN_MGH', startA: 13400, endA: 29900, 
    seqidB: 'KPN_HS11', startB: 10750, endB: 27250, similarity: 93.8 },
  
  // Pseudomonas PA01 vs PA14 - very high synteny (same species)
  { seqidA: 'PAE_PA01', startA: 200, endA: 16800, 
    seqidB: 'PAE_PA14', startB: 250, endB: 16850, similarity: 97.1 },
  { seqidA: 'PAE_PA01', startA: 17000, endA: 26400, 
    seqidB: 'PAE_PA14', startB: 18100, endB: 27500, similarity: 96.5 },
  
  // E. coli vs Klebsiella - moderate synteny (different genera)
  { seqidA: 'ECO_K12', startA: 10700, endA: 22200, 
    seqidB: 'KPN_MGH', startB: 13400, endB: 24900, similarity: 78.3 },
];

Code


import { HoodiniViz } from 'hoodini-viz';
 
<HoodiniViz
  newickStr={newickStr}
  gffFeatures={gffFeatures}
  hoods={hoods}
  proteinLinks={[]}
  nucleotideLinks={nucleotideLinks}
  domainsByGene={{}}
  nucleotideLinkConfig={{ 
    colorBy: 'identity', 
    useAlpha: true, 
    minAlpha: 0.2, 
    maxAlpha: 0.7 
  }}
  showScrollbar={true}
  showRuler={true}
  geneLabelBy="ID"
/>