ArticleMolecular biology and evolution2018
CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- An episodic burst of massive genomic rearrangements and the origin of non-marine annelids.Nature ecology & evolution · 2025Article
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- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach.Scientific reports · 2020Article
- Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition.Genome biology and evolution · 2020Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- Characterization ofFrontiers in genetics · 2020Article
- Article
- Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway.PLoS genetics · 2019Article
- MultiTwin: A Software Suite to Analyze Evolution at Multiple Levels of Organization Using Multipartite Graphs.Genome biology and evolution · 2018Article
- Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.Frontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes evolve by point mutations, but also by shuffling, fusion, and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular data sets, because of computational time. In this article, we present CompositeSearch, a memory-efficient, fast, and scalable method to detect composite gene families in large data sets (typically in the range of several million sequences). CompositeSearch generalizes the use of similarity networks to detect composite and component gene families with a greater recall, accuracy, and precision than recent programs (FusedTriplets and MosaicFinder). Moreover, CompositeSearch provides user-friendly quality descriptions regarding the distribution and primary sequence conservation of these gene families allowing critical biological analyses of these data.
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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.