Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved]
The Orthologous Matrix (OMA) is a method and database that allows users to identify orthologs among many genomes. OMA provides three different types of orthologs: pairwise orthologs, OMA Groups and Hierarchical Orthologous Groups (HOGs). This Primer is organized in two parts. In the first part, we p...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2020-01-01
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| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/9-27/v1 |
| _version_ | 1811222263359340544 |
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| author | Monique Zahn-Zabal Christophe Dessimoz Natasha M. Glover |
| author_facet | Monique Zahn-Zabal Christophe Dessimoz Natasha M. Glover |
| author_sort | Monique Zahn-Zabal |
| collection | DOAJ |
| description | The Orthologous Matrix (OMA) is a method and database that allows users to identify orthologs among many genomes. OMA provides three different types of orthologs: pairwise orthologs, OMA Groups and Hierarchical Orthologous Groups (HOGs). This Primer is organized in two parts. In the first part, we provide all the necessary background information to understand the concepts of orthology, how we infer them and the different subtypes of orthology in OMA, as well as what types of analyses they should be used for. In the second part, we describe protocols for using the OMA browser to find a specific gene and its various types of orthologs. By the end of the Primer, readers should be able to (i) understand homology and the different types of orthologs reported in OMA, (ii) understand the best type of orthologs to use for a particular analysis; (iii) find particular genes of interest in the OMA browser; and (iv) identify orthologs for a given gene. The data can be freely accessed from the OMA browser at https://omabrowser.org. |
| first_indexed | 2024-04-12T08:12:51Z |
| format | Article |
| id | doaj.art-cacaa56e042d42e68be3945c8e4914a3 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-12T08:12:51Z |
| publishDate | 2020-01-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-cacaa56e042d42e68be3945c8e4914a32022-12-22T03:40:55ZengF1000 Research LtdF1000Research2046-14022020-01-01910.12688/f1000research.21508.123697Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved]Monique Zahn-Zabal0Christophe Dessimoz1Natasha M. Glover2Swiss Institute of Bioinformatics, Lausanne, 1015, SwitzerlandSwiss Institute of Bioinformatics, Lausanne, 1015, SwitzerlandDepartment of Computational Biology, University of Lausanne, Lausanne, 1015, SwitzerlandThe Orthologous Matrix (OMA) is a method and database that allows users to identify orthologs among many genomes. OMA provides three different types of orthologs: pairwise orthologs, OMA Groups and Hierarchical Orthologous Groups (HOGs). This Primer is organized in two parts. In the first part, we provide all the necessary background information to understand the concepts of orthology, how we infer them and the different subtypes of orthology in OMA, as well as what types of analyses they should be used for. In the second part, we describe protocols for using the OMA browser to find a specific gene and its various types of orthologs. By the end of the Primer, readers should be able to (i) understand homology and the different types of orthologs reported in OMA, (ii) understand the best type of orthologs to use for a particular analysis; (iii) find particular genes of interest in the OMA browser; and (iv) identify orthologs for a given gene. The data can be freely accessed from the OMA browser at https://omabrowser.org.https://f1000research.com/articles/9-27/v1 |
| spellingShingle | Monique Zahn-Zabal Christophe Dessimoz Natasha M. Glover Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] F1000Research |
| title | Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] |
| title_full | Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] |
| title_fullStr | Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] |
| title_full_unstemmed | Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] |
| title_short | Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] |
| title_sort | identifying orthologs with oma a primer version 1 peer review 2 approved |
| url | https://f1000research.com/articles/9-27/v1 |
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