UPDATE: Zenodo migration postponed to Oct 13 from 06:00-08:00 UTC. Read the announcement.

Software Open Access

g4dbr: A database of validated DNA G-quadruplexes structures in native mass spectrometry conditions

Anirban Ghosh; Eric Largy; Valérie Gabelica

This release includes the production-ready g4db application, and a database file gathering 28 G-quadruplex forming sequences.


Creation, vizualisation, and reporting of curated circular dichroism (CD), 1H-NMR, UV-melting and native mass spectrometry (MS) data from oligonucleotides.
g4dbr includes a number of functionalities that can be utilized outside of this scope, i.e.

  • automated or semi-automated data filtering, treatment and labeling,
  • computation of molar extinction coefficient (λ = 260 nm) of oligonucleotides (epsilon.calculator),
  • UV-melting data treatment (meltR),
  • MS data size reduction (mass.diet)
  • Database file selective data deletion (database.eraser)

Main features

  • Vizualisation of CD, UV-melting, 1H-NMR and native MS data gathered in a database (.Rda format)
    • Collapsible and tabulated interface
    • Quick and user-friendly data filtering in tables and figures (e.g. oligonucleotide, buffer, cation, x-axis range,...)
      • Automated buffer list collection
      • Automated tune and replicate collection
    • Control over the database content, display, and reporting (see below)
  • Robust database creation and edition
    • Data imported from a templated Excel files
    • Selective data importing (by e.g. technique/oligo/buffer/data range)
    • Duplicate detection/suppression
    • Automated deposition date and DOI link generation for traceability purpose
    • Manages replication for MS and UV-melting data
    • Manages tuning for MS data
  • Automated data treatment
    • Conversion of CD to molar ellipticities
    • MS data normalization
    • 1H-NMR and MS peak labelling
    • UV-melting data normalization and conversion to folded fraction
    • UV-melting Tm labeling
  • Custom figures
    • Control over colors, size, and transparency of figures
    • Color palettes adapted to qualitative, sequential, and diverging data
    • Switch between overlaid and paneled figures for quick comparisons
    • Control over variables mapped in paneled figures
    • Automated colour mapping to non-paneled variables
    • Automated figure dimension change to accomodate multiple rows
  • Automated report generation
    • Full or SI dedicated reports
    • pdf, HTML and Word formats can be selected
    • All data, figure captions, figure sizing, file name, etc. generated dynamically without user input
  • Open
    • Easy-to-export data tables (practical for standalone data treatment)
    • Import template easy to read in other software

New in release

version 1.0.0

  • Completed database with 28 G-quadruplex forming sequences
  • Minor app corrections

version 0.2.0

  • MS data now also displayed with a zoomed spectrum
    • Focuses on a selected charge state (default: 5-)
  • MS label formatting
  • Database now includes full buffer compositions (including concentrations and pHs)
  • UV-melting plots x-axis and Tm labels switch from Kelvin to °C
  • Minor corrections/enhancements in SI report
Files (66.4 MB)
Name Size
66.4 MB Download
All versions This version
Views 227227
Downloads 1010
Data volume 664.1 MB664.1 MB
Unique views 187187
Unique downloads 1010


Cite as