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Updated: Jan 22, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction
Fabian Sievers1, Desmond G Higgins1
1Conway Institute, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
Motivation:
Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest.
Results:
We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks.
Availability And Implementation:
QuanTest2 is available at http://bioinf.ucd.ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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