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. 2016 Jul 1;32(13):2053-5.
doi: 10.1093/bioinformatics/btw122. Epub 2016 Mar 7.

ORFanFinder: automated identification of taxonomically restricted orphan genes

Alex Ekstrom  1 , Yanbin Yin  2
Affiliations

ORFanFinder: automated identification of taxonomically restricted orphan genes

Alex Ekstrom et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Pseudocodes of the algorithm
See this image and copyright information in PMC

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