ReviewNucleic acids research2010
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.
Review in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 2 of them syntheses that pooled it.
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Who cites it
33 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
- Guidelines for benchmarking of optimization-based approaches for fitting mathematical models.Genome biology · 2019Guideline
- BEST: Basic Embedding Search Tool Enhancing Discovery of Novel Enzyme.Interdisciplinary sciences, computational life sciences · 2026Article
- Fast, sensitive detection of protein homologs using deep dense retrieval.Nature biotechnology · 2025Article
- ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation.International journal of molecular sciences · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- ViLoN-a multi-layer network approach to data integration demonstrated for patient stratification.Nucleic acids research · 2023Article
- The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.PloS one · 2023Article
- Accuracy and Completeness of Long Read Metagenomic Assemblies.Microorganisms · 2022Article
- Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families.NAR genomics and bioinformatics · 2022Article
- Developments in Algorithms for Sequence Alignment: A Review.Biomolecules · 2022Review
- RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.RNA (New York, N.Y.) · 2020Article
- Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study.The Egyptian journal of medical human genetics · 2020Article
- Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods.Computational and structural biotechnology journal · 2020Review
- Essential guidelines for computational method benchmarking.Genome biology · 2019Review
- Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets.Systematic biology · 2019Article
- Systematic benchmarking of omics computational tools.Nature communications · 2019Review
- A benchmark study of sequence alignment methods for protein clustering.BMC bioinformatics · 2018Article
- The fractured landscape of RNA-seq alignment: the default in our STARs.Nucleic acids research · 2018Article
- Benchmarking the next generation of homology inference tools.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The post-genomic era presents many new challenges for the field of bioinformatics. Novel computational approaches are now being developed to handle the large, complex and noisy datasets produced by high throughput technologies. Objective evaluation of these methods is essential (i) to assure high quality, (ii) to identify strong and weak points of the algorithms, (iii) to measure the improvements introduced by new methods and (iv) to enable non-specialists to choose an appropriate tool. Here, we discuss the development of formal benchmarks, designed to represent the current problems encountered in the bioinformatics field. We consider several criteria for building good benchmarks and the advantages to be gained when they are used intelligently. To illustrate these principles, we present a more detailed discussion of benchmarks for multiple alignments of protein sequences. As in many other domains, significant progress has been achieved in the multiple alignment field and the datasets have become progressively more challenging as the existing algorithms have evolved. Finally, we propose directions for future developments that will ensure that the bioinformatics benchmarks correspond to the challenges posed by the high throughput data.
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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.