ArticleGenome research2011
Cactus: Algorithms for genome multiple sequence alignment.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
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- Annotating the genome at single-nucleotide resolution with DNA foundation models.Nature methods · 2025Article
- Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
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- FastGA: fast genome alignment.Bioinformatics advances · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera.Genome biology and evolution · 2024Article
- Novel Sex-Specific Genes and Diverse Interspecific Expression in the Antennal Transcriptomes of Ithomiine Butterflies.Genome biology and evolution · 2024Article
- Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model.bioRxiv : the preprint server for biology · 2024Article
- Article
86 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new "Cactus" alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.
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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.