ORFanID is a web-based software engine that identifies ORFan genes from the genomes of specified species or from a given list of DNA sequences. The scope of the search for orphan genes can be defined by the selection of the taxonomy level of interest. Detectable homologous sequences are found for candidate gene in the NCBI databases. From these findings the ORFanID engine identifies and depicts orphan genes. Results may be viewed and analyzed graphically for the purpose of scientific research and inquiry.
Orphan genes (also known as taxonomically restricted genes) are genes that do not have related ancestral genes in other species or at the specified taxonomy level. At the molecular level, ORFan genes consist of DNA sequences that have no homology with sequences found in common DNA databases such as Genbank. While the prevailing dogma has defined genes in different species as a result of gene duplication or recombination, the presence of orphan gene ubiquity in various sequenced genomes is a mystery, perhaps even a significant problem to be solved.
Historically, gene function is known to be expressed through proteins. There are specific organisms that have been found with unique proteins expressed by orphan genes such as Hydra, various Mollusks, Salamander and others. It appears that the anatomy of Hydra is mediated by orphan genes that give rise to unique proteins. Similarly, the mantle of various Mollusks has been found to be expressed from orphan genes, while the regeration of salamander limbs are mediated by orphans (Dr. Paul Nelson, 2017)
By identifying these unique DNA sequences, ORFanID can help discover the origin, function and other significance of orphan genes. The software is able to identify genes unique to genus, family, or species etc. at differing taxonomy levels. Based on the parameters specified, some of orphans (also called Taxonomy Restricted Genes) may or may not fall under the given classification for strict ORFans. As such, ORFanID can help delineate the actual sequence and function of de novo genes discovered in species and at all levels of the taxonomy tree.