ArticleGenome research2020
The multicomparative 2-n-way genome suite.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Unearthing the secrets of Australia's most enigmatic and cryptic mammal, the marsupial mole.Science advances · 2025Article
- Interspecific Comparison of Orthologous Short Interspersed Elements Loci Using Whole-Genome Data.Genes · 2023Article
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- The successive emergence of ERVL-MaLRs in primates.Virus evolution · 2023Article
- Reunion of Australasian Possums by Shared SINE Insertions.Systematic biology · 2022Article
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- Methodologies for theGenes · 2022Review
- Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.Genome biology and evolution · 2022Article
- Gene Conversion amongstGenes · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, in which user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups. Thus, the 2-n-way software suite is ideal for performing multidirectional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose approximately 100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.
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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.