ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.
With the numerous genomes sequenced today, it has been revealed that a noteworthy percentage of genes in a given taxon of organisms in the phylogenetic tree of life do not have orthologous sequences in other taxa. These sequences are commonly referred to as "orphans" or "ORFans"...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0291260&type=printable |
| _version_ | 1827151323697512448 |
|---|---|
| author | Richard S Gunasekera Komal K B Raja Suresh Hewapathirana Emanuel Tundrea Vinodh Gunasekera Thushara Galbadage Paul A Nelson |
| author_facet | Richard S Gunasekera Komal K B Raja Suresh Hewapathirana Emanuel Tundrea Vinodh Gunasekera Thushara Galbadage Paul A Nelson |
| author_sort | Richard S Gunasekera |
| collection | DOAJ |
| description | With the numerous genomes sequenced today, it has been revealed that a noteworthy percentage of genes in a given taxon of organisms in the phylogenetic tree of life do not have orthologous sequences in other taxa. These sequences are commonly referred to as "orphans" or "ORFans" if found as single occurrences in a single species or as "taxonomically restricted genes" (TRGs) when found at higher taxonomic levels. Quantitative and collective studies of these genes are necessary for understanding their biological origins. However, the current software for identifying orphan genes is limited in its functionality, database search range, and very complex algorithmically. Thus, researchers studying orphan genes must harvest their data from many disparate sources. ORFanID is a graphical web-based search engine that facilitates the efficient identification of both orphan genes and TRGs at all taxonomic levels, from DNA or amino acid sequences in the NCBI database cluster and other large bioinformatics repositories. The software allows users to identify genes that are unique to any taxonomic rank, from species to domain, using NCBI systematic classifiers. It provides control over NCBI database search parameters, and the results are presented in a spreadsheet as well as a graphical display. The tables in the software are sortable, and results can be filtered using the fuzzy search functionality. The visual presentation can be expanded and collapsed by the taxonomic tree to its various branches. Example results from searches on five species and gene expression data from specific orphan genes are provided in the Supplementary Information. |
| first_indexed | 2024-03-11T15:21:59Z |
| format | Article |
| id | doaj.art-5b51d4ede3174873a656bec0c9cd1a04 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2025-03-20T21:48:09Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5b51d4ede3174873a656bec0c9cd1a042024-08-11T05:33:12ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-011810e029126010.1371/journal.pone.0291260ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.Richard S GunasekeraKomal K B RajaSuresh HewapathiranaEmanuel TundreaVinodh GunasekeraThushara GalbadagePaul A NelsonWith the numerous genomes sequenced today, it has been revealed that a noteworthy percentage of genes in a given taxon of organisms in the phylogenetic tree of life do not have orthologous sequences in other taxa. These sequences are commonly referred to as "orphans" or "ORFans" if found as single occurrences in a single species or as "taxonomically restricted genes" (TRGs) when found at higher taxonomic levels. Quantitative and collective studies of these genes are necessary for understanding their biological origins. However, the current software for identifying orphan genes is limited in its functionality, database search range, and very complex algorithmically. Thus, researchers studying orphan genes must harvest their data from many disparate sources. ORFanID is a graphical web-based search engine that facilitates the efficient identification of both orphan genes and TRGs at all taxonomic levels, from DNA or amino acid sequences in the NCBI database cluster and other large bioinformatics repositories. The software allows users to identify genes that are unique to any taxonomic rank, from species to domain, using NCBI systematic classifiers. It provides control over NCBI database search parameters, and the results are presented in a spreadsheet as well as a graphical display. The tables in the software are sortable, and results can be filtered using the fuzzy search functionality. The visual presentation can be expanded and collapsed by the taxonomic tree to its various branches. Example results from searches on five species and gene expression data from specific orphan genes are provided in the Supplementary Information.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0291260&type=printable |
| spellingShingle | Richard S Gunasekera Komal K B Raja Suresh Hewapathirana Emanuel Tundrea Vinodh Gunasekera Thushara Galbadage Paul A Nelson ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes. PLoS ONE |
| title | ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes. |
| title_full | ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes. |
| title_fullStr | ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes. |
| title_full_unstemmed | ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes. |
| title_short | ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes. |
| title_sort | orfanid a web based search engine for the discovery and identification of orphan and taxonomically restricted genes |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0291260&type=printable |
| work_keys_str_mv | AT richardsgunasekera orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes AT komalkbraja orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes AT sureshhewapathirana orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes AT emanueltundrea orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes AT vinodhgunasekera orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes AT thusharagalbadage orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes AT paulanelson orfanidawebbasedsearchengineforthediscoveryandidentificationoforphanandtaxonomicallyrestrictedgenes |