School/Department
School of Science Technology and Health
Publication Date
2-2022
Abstract
With the multiplicity of genomes sequenced today, it has been shown that significant percentages of genes in any given taxon do not possess orthologous sequences in other taxa. These sequences are typically designated as orphans/ORFans when found as singletons in one species only or taxonomically restricted genes (TRGs) when found at higher taxonomic ranks. Quantitative and collective studies of these genes are necessary for understanding their biological origins. Currently, orphan gene identifying software is limited, and those previously available are either not functional, are limited in their database search range, or are very complex algorithmically. Thus, an interested researcher studying orphan genes must harvest their data from many disparate sources. ORFanID is a graphical web-based search engine that efficiently finds both orphan genes and TRGs at all taxonomic levels, from DNA or amino acid sequences in the entire NCBI database cluster and other large bioinformatics repositories. This algorithm allows the easy identification of both orphan genes and TRGs using both nucleotide and protein sequences in any species of interest. ORFanID identifies genes unique to any taxonomic rank, from species to a domain, using standard NCBI systematic classifiers. The software allows for user control of the NCBI database search parameters. The results of the search are provided in a spreadsheet as well as a graphical display. All the tables in the software are sortable by column, and results can be easily filtered with fuzzy search functionality. In addition, the visual presentation is expandable and collapsible by taxonomy.
Keywords
ORFanID; Taxonomically Restricted Genes (TRG); bioinformatics; ortholog
DOI of Published Version
10.1101/2022.02.01.478498
Rights
the authors
Recommended Citation
Gunasekera, Richard S.; Raja, Komal K.B.; Hewapathirana, Suresh; Galbadage, Thushara; Tundrea, Emanuel; Gunasekera, Vinodh; and Nelson, Paul A., "ORFanID: A Web-Based Search Engine for the Discovery and Identification of Orphan and Taxonomically Restricted Genes" (2022). Faculty Articles & Research. 668.
https://digitalcommons.biola.edu/faculty-articles/668
Supplemental
Comments
This is a pre-copy-editing, author-produced PDF of an article submitted/accepted for publication in Frontiers of Genetics: Computational Genomics following peer review. The original paper was submitted for publication in Feb. 2022.