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03 Database

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Charlie Bayne edited this page Mar 28, 2026 · 1 revision

Database

The Database tab visualizes the taxonomic composition of your search database and shows how well each organism is represented in your data.

Summary Statistics

Three value boxes at the top display:

  • Number of samples in the experiment
  • Number of species detected across the dataset
  • Number of protein groups detected

Taxonomic Tree

An interactive network graph showing all taxa in the database and how they are hierarchically related. Nodes represent taxonomic units; edges represent parent-child relationships in the taxonomy.

You can adjust the layout algorithm used to render the tree. Available layouts include:

  • Reingold-Tilford
  • Fruchterman-Reingold
  • Kamada-Kawai
  • and several others

This visualization is useful for understanding the breadth and composition of the organism database used during the Conduit-Ascent search.

Protein Coverage Table

An interactive table showing per-species protein detection statistics, including:

  • Species name
  • Number of proteins detected
  • Number of proteins present in the database
  • Percent coverage

The table can be downloaded for use outside the app.

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