SMORE: Synteny Modulator of Repetitive Elements
Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2017-10-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/7/4/42 |
| _version_ | 1811187805237280768 |
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| author | Sarah J. Berkemer Anne Hoffmann Cameron R. A. Murray Peter F. Stadler |
| author_facet | Sarah J. Berkemer Anne Hoffmann Cameron R. A. Murray Peter F. Stadler |
| author_sort | Sarah J. Berkemer |
| collection | DOAJ |
| description | Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available. |
| first_indexed | 2024-04-11T14:09:47Z |
| format | Article |
| id | doaj.art-fa947f72a87d489abf3927c9055d6015 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-04-11T14:09:47Z |
| publishDate | 2017-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-fa947f72a87d489abf3927c9055d60152022-12-22T04:19:46ZengMDPI AGLife2075-17292017-10-01744210.3390/life7040042life7040042SMORE: Synteny Modulator of Repetitive ElementsSarah J. Berkemer0Anne Hoffmann1Cameron R. A. Murray2Peter F. Stadler3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, GermanyBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, GermanyDepartment of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, CanadaBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, GermanySeveral families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available.https://www.mdpi.com/2075-1729/7/4/42bioinformaticspipelineworkflowconcerted evolutionsyntenyorthologytandem duplicationsY RNAstRNAs |
| spellingShingle | Sarah J. Berkemer Anne Hoffmann Cameron R. A. Murray Peter F. Stadler SMORE: Synteny Modulator of Repetitive Elements Life bioinformatics pipeline workflow concerted evolution synteny orthology tandem duplications Y RNAs tRNAs |
| title | SMORE: Synteny Modulator of Repetitive Elements |
| title_full | SMORE: Synteny Modulator of Repetitive Elements |
| title_fullStr | SMORE: Synteny Modulator of Repetitive Elements |
| title_full_unstemmed | SMORE: Synteny Modulator of Repetitive Elements |
| title_short | SMORE: Synteny Modulator of Repetitive Elements |
| title_sort | smore synteny modulator of repetitive elements |
| topic | bioinformatics pipeline workflow concerted evolution synteny orthology tandem duplications Y RNAs tRNAs |
| url | https://www.mdpi.com/2075-1729/7/4/42 |
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