ArticleBioinformatics (Oxford, England)2016
ORFanFinder: automated identification of taxonomically restricted orphan genes.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.PloS one · 2023Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
- Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree.BMC bioinformatics · 2021Article
- Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution.Frontiers in plant science · 2020Article
- Reanalysis ofMicroorganisms · 2019Article
- Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches.mSystems · 2019Article
- Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
motivationOrphan genes, also known as ORFans, are newly evolved genes in a genome that enable the organism to adapt to specific living environment. The gene content of every sequenced genome can be classified into different age groups, based on how widely/narrowly a gene's homologs are distributed in the context of species taxonomy. Those having homologs restricted to organisms of particular taxonomic ranks are classified as taxonomically restricted ORFans.
resultsImplementing this idea, we have developed an open source program named ORFanFinder and a free web server to allow automated classification of a genome's gene content and identification of ORFans at different taxonomic ranks. ORFanFinder and its web server will contribute to the comparative genomics field by facilitating the study of the origin of new genes and the emergence of lineage-specific traits in both prokaryotes and eukaryotes. AVAILABILITY AND IMPLEMENTATION: http://cys.bios.niu.edu/orfanfinder CONTACT: yyin@niu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.