ArticleBMC bioinformatics2006
The accuracy of several multiple sequence alignment programs for proteins.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 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
59 citing papers in PubMed, 170 citations in OpenAlex.
- DiMA: sequence diversity dynamics analyser for viruses.Briefings in bioinformatics · 2024Article
- Article
- Allosteric regulation of kinase activity in living cells.bioRxiv : the preprint server for biology · 2023Article
- Genetic Analysis of Orf Virus (ORFV) Strains Isolated from Goats in China: Insights into Epidemiological Characteristics and Evolutionary Patterns.Virus research · 2023Article
- Article
- Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features.Nucleic acids research · 2023Article
- Coemergence of the Amphipathic Helix on Ameloblastin With Mammalian Prismatic Enamel.Molecular biology and evolution · 2022Article
- Protein Structure Prediction: Conventional and Deep Learning Perspectives.The protein journal · 2021Review
- Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity.BMC evolutionary biology · 2019Article
- Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction.Systematic biology · 2019Article
- A benchmark study of sequence alignment methods for protein clustering.BMC bioinformatics · 2018Article
- Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.Genome biology and evolution · 2017Article
- Biocuration in the structure-function linkage database: the anatomy of a superfamily.Database : the journal of biological databases and curation · 2017Article
- Structural Determinants of Sleeping Beauty Transposase Activity.Molecular therapy : the journal of the American Society of Gene Therapy · 2016Article
- ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.Nucleic acids research · 2016Article
- Consensus protein design.Protein engineering, design & selection : PEDS · 2016Review
- Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database.SpringerPlus · 2016Article
- Computational approaches to study the effects of small genomic variations.Journal of molecular modeling · 2015Review
- Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors.BMC bioinformatics · 2015Article
- Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix.BMC bioinformatics · 2015Article
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 at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs.
resultsWe tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30,000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the results relative to BAliBASE- and Simprot-generated data sets were consistent in most cases.
conclusionOur results indicate that employing Simprot's simulated sequences allows the creation of a more flexible and broader range of alignment classes than the usual methods for alignment accuracy assessment. Simprot also allows for a quick and efficient analysis of a wider range of possible evolutionary histories that might not be present in currently available alignment sets. Among the nine programs tested, the iterative approach available in Mafft (L-INS-i) and ProbCons were consistently the most accurate, with Mafft being the faster of the two.
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.