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

Authors: Anirban Ghosh; Largy, Eric; Gabelica, Valérie;

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

Abstract

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

Keywords

nucleic acids, mass spectrometry,, G-quadruplex, data treatment, biophysics, UV-melting, R, DNA, NMR, database, circular dichroism

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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