FUSTr: a tool to find gene families under selection in transcriptomes
Background The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. T...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2018-01-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/4234.pdf |
| _version_ | 1797425562823688192 |
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| author | T. Jeffrey Cole Michael S. Brewer |
| author_facet | T. Jeffrey Cole Michael S. Brewer |
| author_sort | T. Jeffrey Cole |
| collection | DOAJ |
| description | Background The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. This is a tool that finds genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. Results When applied to previously studied spider transcriptomic data as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection in relatively little time. Conclusions FUSTr provides a useful tool for novice bioinformaticians to characterize the molecular evolution of organisms throughout the tree of life using large transcriptomic biodiversity datasets and can utilize multi-processor high-performance computational facilities. |
| first_indexed | 2024-03-09T08:17:54Z |
| format | Article |
| id | doaj.art-ac1fb323d49e443d9c78917891ecf6b5 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:17:54Z |
| publishDate | 2018-01-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-ac1fb323d49e443d9c78917891ecf6b52023-12-02T22:00:34ZengPeerJ Inc.PeerJ2167-83592018-01-016e423410.7717/peerj.4234FUSTr: a tool to find gene families under selection in transcriptomesT. Jeffrey Cole0Michael S. Brewer1Department of Biology, East Carolina University, Greenville, NC, United States of AmericaDepartment of Biology, East Carolina University, Greenville, NC, United States of AmericaBackground The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. This is a tool that finds genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. Results When applied to previously studied spider transcriptomic data as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection in relatively little time. Conclusions FUSTr provides a useful tool for novice bioinformaticians to characterize the molecular evolution of organisms throughout the tree of life using large transcriptomic biodiversity datasets and can utilize multi-processor high-performance computational facilities.https://peerj.com/articles/4234.pdfTranscriptomicsPositive selectionMolecular evolutionGene family reconstruction |
| spellingShingle | T. Jeffrey Cole Michael S. Brewer FUSTr: a tool to find gene families under selection in transcriptomes PeerJ Transcriptomics Positive selection Molecular evolution Gene family reconstruction |
| title | FUSTr: a tool to find gene families under selection in transcriptomes |
| title_full | FUSTr: a tool to find gene families under selection in transcriptomes |
| title_fullStr | FUSTr: a tool to find gene families under selection in transcriptomes |
| title_full_unstemmed | FUSTr: a tool to find gene families under selection in transcriptomes |
| title_short | FUSTr: a tool to find gene families under selection in transcriptomes |
| title_sort | fustr a tool to find gene families under selection in transcriptomes |
| topic | Transcriptomics Positive selection Molecular evolution Gene family reconstruction |
| url | https://peerj.com/articles/4234.pdf |
| work_keys_str_mv | AT tjeffreycole fustratooltofindgenefamiliesunderselectionintranscriptomes AT michaelsbrewer fustratooltofindgenefamiliesunderselectionintranscriptomes |