ArticleNucleic acids research2012
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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138 citing papers in PubMed.
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- Fusion, fission, and scrambling of the bilaterian genome in Bryozoa.Genome research · 2025Article
- Comparative genomics reveals the genomic basis of race T2 emergence and heavy metal resistance inFrontiers in microbiology · 2025Article
78 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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Abstract
Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein-protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.
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