ArticleNucleic acids research2008
An approach of orthology detection from homologous sequences under minimum evolution.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 27 citations in OpenAlex.
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- Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation.Scientific reports · 2019Article
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- Comparative genomic analysis ofGenes & genomics · 2018Article
- A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation.Frontiers in genetics · 2017Article
- Comparative genomic analysis reveals genetic features related to the virulence ofGut pathogens · 2017Article
- HGTree: database of horizontally transferred genes determined by tree reconciliation.Nucleic acids research · 2016Article
- Inferring Orthologs: Open Questions and Perspectives.Genomics insights · 2016Review
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- An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species.BioMed research international · 2015Article
- Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.BMC evolutionary biology · 2012Article
- Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.Genome biology and evolution · 2012Article
- Benefits of using molecular structure and abundance in phylogenomic analysis.Frontiers in genetics · 2012Article
- Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.Nucleic acids research · 2011Article
- A genome-wide identification of genes potentially associated with host specificity of Brucella species.Journal of microbiology (Seoul, Korea) · 2011Article
- The proteomic complexity and rise of the primordial ancestor of diversified life.BMC evolutionary biology · 2011Article
- Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.PLoS biology · 2010Article
- AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences.Algorithms for molecular biology : AMB · 2010Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the field of phylogenetics and comparative genomics, it is important to establish orthologous relationships when comparing homologous sequences. Due to the slight sequence dissimilarity between orthologs and paralogs, it is prone to regarding paralogs as orthologs. For this reason, several methods based on evolutionary distance, phylogeny and BLAST have tried to detect orthologs with more precision. Depending on their algorithmic implementations, each of these methods sometimes has increased false negative or false positive rates. Here, we developed a novel algorithm for orthology detection that uses a distance method based on the phylogenetic criterion of minimum evolution. Our algorithm assumes that sets of sequences exhibiting orthologous relationships are evolutionarily less costly than sets that include one or more paralogous relationships. Calculation of evolutionary cost requires the reconstruction of a neighbor-joining (NJ) tree, but calculations are unaffected by the topology of any given NJ tree. Unlike tree reconciliation, our algorithm appears free from the problem of incorrect topologies of species and gene trees. The reliability of the algorithm was tested in a comparative analysis with two other orthology detection methods using 95 manually curated KOG datasets and 21 experimentally verified EXProt datasets. Sensitivity and specificity estimates indicate that the concept of minimum evolution could be valuable for the detection of orthologs.
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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.