ReviewBriefings in bioinformatics2011
Ortholog identification in the presence of domain architecture rearrangement.
Review in Briefings in bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- PharaohFUN: phylogenomic analysis for plant protein history and function elucidation.Molecular biology and evolution · 2026Article
- The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.Evolution letters · 2024Article
- Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events.Frontiers in bioinformatics · 2023Article
- A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases.Biochemistry · 2019Article
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.Nucleic acids research · 2019Article
- Automated selection of homologs to track the evolutionary history of proteins.BMC bioinformatics · 2018Article
- Uniclust databases of clustered and deeply annotated protein sequences and alignments.Nucleic acids research · 2017Article
- PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.Database : the journal of biological databases and curation · 2016Article
- Inferring Orthologs: Open Questions and Perspectives.Genomics insights · 2016Review
- Domain similarity based orthology detection.BMC bioinformatics · 2015Article
- Article
- Big data and other challenges in the quest for orthologs.Bioinformatics (Oxford, England) · 2014Article
- Evolution and classification of myosins, a paneukaryotic whole-genome approach.Genome biology and evolution · 2014Article
- Article
- SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.Bioinformatics (Oxford, England) · 2013Article
- The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.Nucleic acids research · 2013Article
- Identification of MFS proteins in sorghum using semantic similarity.Theory in biosciences = Theorie in den Biowissenschaften · 2013Article
- Functional and evolutionary implications of gene orthology.Nature reviews. Genetics · 2013Review
- The interface of protein structure, protein biophysics, and molecular evolution.Protein science : a publication of the Protein Society · 2012Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ortholog identification is used in gene functional annotation, species phylogeny estimation, phylogenetic profile construction and many other analyses. Bioinformatics methods for ortholog identification are commonly based on pairwise protein sequence comparisons between whole genomes. Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain but differ outside this region of homology. While promiscuous domains represent a challenge to all orthology prediction methods, overall structural similarity is highly correlated with proximity in a phylogenetic tree, conferring a degree of robustness to phylogenetic methods. In this article, we review the issues involved in orthology prediction when data sets include sequences with structurally heterogeneous domain architectures, with particular attention to automated methods designed for high-throughput application, and present a case study to illustrate the challenges in this area.
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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.