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

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

Scope

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