Alex Ekstrom1, Yanbin Yin2. 1. Department of Computer Science. 2. Department of Biological Sciences, Montgomery Hall 325A, Northern Illinois University, DeKalb, IL, USA.
Abstract
MOTIVATION: Orphan 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. RESULTS: Implementing 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.
MOTIVATION: Orphan 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. RESULTS: Implementing 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.
Authors: Konstantin Khalturin; Georg Hemmrich; Sebastian Fraune; René Augustin; Thomas C G Bosch Journal: Trends Genet Date: 2009-08-27 Impact factor: 11.639
Authors: Anne-Ruxandra Carvunis; Thomas Rolland; Ilan Wapinski; Michael A Calderwood; Muhammed A Yildirim; Nicolas Simonis; Benoit Charloteaux; César A Hidalgo; Justin Barbette; Balaji Santhanam; Gloria A Brar; Jonathan S Weissman; Aviv Regev; Nicolas Thierry-Mieg; Michael E Cusick; Marc Vidal Journal: Nature Date: 2012-07-19 Impact factor: 49.962