ArticleNucleic acids research2017
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- Learning genotype-phenotype associations from gaps in multi-species sequence alignments.Briefings in bioinformatics · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.Molecular biology and evolution · 2021Article
- Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences.Evolutionary bioinformatics online · 2020Article
- The Evolutionary Traceability of a Protein.Genome biology and evolution · 2019Article
- Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction.Systematic biology · 2019Article
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5 authors.
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Abstract
Many analyses for the detection of biological phenomena rely on a multiple sequence alignment as input. The results of such analyses are often further studied through parametric bootstrap procedures, using sequence simulators. One of the problems with conducting such simulation studies is that users currently have no means to decide which insertion and deletion (indel) parameters to choose, so that the resulting sequences mimic biological data. Here, we present SpartaABC, a web server that aims to solve this issue. SpartaABC implements an approximate-Bayesian-computation rejection algorithm to infer indel parameters from sequence data. It does so by extracting summary statistics from the input. It then performs numerous sequence simulations under randomly sampled indel parameters. By computing a distance between the summary statistics extracted from the input and each simulation, SpartaABC retains only parameters behind simulations close to the real data. As output, SpartaABC provides point estimates and approximate posterior distributions of the indel parameters. In addition, SpartaABC allows simulating sequences with the inferred indel parameters. To this end, the sequence simulators, Dawg 2.0 and INDELible were integrated. Using SpartaABC we demonstrate the differences in indel dynamics among three protein-coding genes across mammalian orthologs. SpartaABC is freely available for use at http://spartaabc.tau.ac.il/webserver.
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