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August 2021 Update

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@persalteas persalteas released this 18 Aug 08:07
v1.6-beta
60f0af5

v 1.6 beta, August 2021

Aglaé Tabot joins the development team. Khodor Hannoush leaves.

FEATURE CHANGES

  • Distinct options --cmalign-opts and --cmalign-rrna-opts allow to adapt the parameters for LSU and SSU families.
    The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow,
    requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families.
  • The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed.
  • Distances matrices are computed on all availables molecules of the family by default, but you can use statistics.py --non-redundant to only
    select the equivalence class representatives at a given resolution into account (new option). For storage reasons, rRNAs are always run in
    this mode (but this might change in the future : space required is 'only' ~300 GB).
  • We now provide for download the renumbered (standardized) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database.
  • We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed).
  • statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters, measured on the unmapped data at a given resolution threshold.
    The parameters include:
    • All atom bonded distances and torsion angles
    • Distances, flat angles and torsion angles in the Pyle/VFold model
    • Distances, flat angles and torsion anfles in the HiRE-RNA model
    • Sequence-dependant geometric parameters of the basepairs for all non-canonical basepairs in the HiRE-RNA model.

The data is saved as JSON files of parameters, and numerous figures are produced to illustrate the distributions.
The number of gaussians to use in the GMMs are hard-coded in geometric_stats.py after our first estimation. If you do not want to trust this estimation, you can ignore it with option --rescan-nmodes. An exploration of the number of Gaussians from 1 to 8 will be performed, and the best GMM will be kept.

BUG CORRECTIONS

  • Many small fixes, leading to the support of many previously "known issues"
  • Performance tweaks

TECHNICAL CHANGES

  • New code file geometric_stats.py
  • New automation script that starts from scratch
  • Switched to DSSR Pro.
  • Switched to esl-alimerge instead of cmalign --merge to merge alignments.
  • Tested successfully with Python 3.9.6 + BioPython 1.79.
    However, the production server still runs with Python 3.8.1 + BioPython 1.78.
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