ArticleBioinformatics (Oxford, England)2020
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Sequence analysis of the hepatitis D virus across genotypes reveals highly conserved regions amidst evidence of recombination.Virus evolution · 2025Article
- Development of radiofluorinated MLN-4760 derivatives for PET imaging of the SARS-CoV-2 entry receptor ACE2.European journal of nuclear medicine and molecular imaging · 2024Article
- DiMA: sequence diversity dynamics analyser for viruses.Briefings in bioinformatics · 2024Article
- A computational strategy to improve the activity of tyrosine phenol-lyase for the synthesis of L-DOPA.Scientific reports · 2024Article
- Comparative Analysis of Dehydrins from Woody Plant Species.Biomolecules · 2024Article
- Leveraging protein language models for accurate multiple sequence alignments.Genome research · 2023Article
- Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization.PLoS pathogens · 2023Article
- Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA.RNA (New York, N.Y.) · 2022Article
- Deep learning for protein secondary structure prediction: Pre and post-AlphaFold.Computational and structural biotechnology journal · 2022Review
- Article
- Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench.Genome biology and evolution · 2020Article
- RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.RNA (New York, N.Y.) · 2020Article
- Deep learning methods in protein structure prediction.Computational and structural biotechnology journal · 2020Review
- Kalign 3: multiple sequence alignment of large data sets.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationSecondary 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.
resultsWe 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.