ArticleMolecular biology and evolution2009
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.
Article in Molecular biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 53 citations in OpenAlex.
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- Simulating domain architecture evolution.Bioinformatics (Oxford, England) · 2022Article
- From pairwise to multiple spliced alignment.Bioinformatics advances · 2022Article
- The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.Systematic biology · 2021Article
- SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution.BMC bioinformatics · 2019Article
- ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models.eLife · 2019Article
- SAliBASE: A Database of Simulated Protein Alignments.Evolutionary bioinformatics online · 2019Review
- Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.Journal of molecular evolution · 2018Article
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
- General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation.BMC bioinformatics · 2016Article
- General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?BMC bioinformatics · 2016Article
- Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.BMC bioinformatics · 2016Article
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
- πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.BMC bioinformatics · 2014Article
- Article
- Evaluating the accuracy and efficiency of multiple sequence alignment methods.Evolutionary bioinformatics online · 2014Article
- Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0.Ecology and evolution · 2013Article
- Computer programs and methodologies for the simulation of DNA sequence data with recombination.Frontiers in genetics · 2013Article
- Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features.Nucleic acids research · 2012Article
- Simulation of molecular data under diverse evolutionary scenarios.PLoS computational biology · 2012Article
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4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Sequence simulation is an important tool in validating biological hypotheses as well as testing various bioinformatics and molecular evolutionary methods. Hypothesis testing relies on the representational ability of the sequence simulation method. Simple hypotheses are testable through simulation of random, homogeneously evolving sequence sets. However, testing complex hypotheses, for example, local similarities, requires simulation of sequence evolution under heterogeneous models. To this end, we previously introduced indel-Seq-Gen version 1.0 (iSGv1.0; indel, insertion/deletion). iSGv1.0 allowed heterogeneous protein evolution and motif conservation as well as insertion and deletion constraints in subsequences. Despite these advances, for complex hypothesis testing, neither iSGv1.0 nor other currently available sequence simulation methods is sufficient. indel-Seq-Gen version 2.0 (iSGv2.0) aims at simulating evolution of highly divergent DNA sequences and protein superfamilies. iSGv2.0 improves upon iSGv1.0 through the addition of lineage-specific evolution, motif conservation using PROSITE-like regular expressions, indel tracking, subsequence-length constraints, as well as coding and noncoding DNA evolution. Furthermore, we formalize the sequence representation used for iSGv2.0 and uncover a flaw in the modeling of indels used in current state of the art methods, which biases simulation results for hypotheses involving indels. We fix this flaw in iSGv2.0 by using a novel discrete stepping procedure. Finally, we present an example simulation of the calycin-superfamily sequences and compare the performance of iSGv2.0 with iSGv1.0 and random model of sequence evolution.
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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.