ArticleGigaScience2019
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 37 citations in OpenAlex.
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- Promoter insertion leads to polyembryony in mango - a case of convergent evolution with citrus.Horticulture research · 2023Article
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- OrthoPhy: A Program to Construct Ortholog Data Sets Using Taxonomic Information.Genome biology and evolution · 2023Article
- Population genomics unravels the Holocene history of bread wheat and its relatives.Nature plants · 2023Article
- Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.Genomics · 2022Article
- Fast characterization of segmental duplication structure in multiple genome assemblies.Algorithms for molecular biology : AMB · 2022Article
- Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.Nucleic acids research · 2022Article
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- A nomenclature for echinoderm genes.Database : the journal of biological databases and curation · 2021Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes.Briefings in bioinformatics · 2021Article
- Integration of 1:1 orthology maps and updated datasets into Echinobase.Database : the journal of biological databases and curation · 2021Article
- The evolution of coloration and opsins in tarantulas.Proceedings. Biological sciences · 2020Article
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- Discovery of multi-operon colinear syntenic blocks in microbial genomes.Bioinformatics (Oxford, England) · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene homology type classification is required for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. Consequently, a large variety of tools have been developed to perform homology classification across genomes of different species. However, when applied to large genomic data sets, these tools require high memory and CPU usage, typically available only in computational clusters.
findingsHere we present a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data. SwiftOrtho uses long k-mers to speed up homology search, while using a reduced amino acid alphabet and spaced seeds to compensate for the loss of sensitivity due to long k-mers. In addition, it uses an affinity propagation algorithm to reduce the memory usage when clustering large-scale orthology relationships into orthologous groups. In our tests, SwiftOrtho was the only tool that completed orthology analysis of proteins from 1,760 bacterial genomes on a computer with only 4 GB RAM. Using various standard orthology data sets, we also show that SwiftOrtho has a high accuracy.
conclusionsSwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low-memory computers. SwiftOrtho is available at https://github.com/Rinoahu/SwiftOrtho.
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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.