Revising transcriptome assemblies with phylogenetic information.
A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as c...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0244202 |
| _version_ | 1818899694130036736 |
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| author | August Guang Mark Howison Felipe Zapata Charles Lawrence Casey W Dunn |
| author_facet | August Guang Mark Howison Felipe Zapata Charles Lawrence Casey W Dunn |
| author_sort | August Guang |
| collection | DOAJ |
| description | A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts. |
| first_indexed | 2024-12-19T19:52:02Z |
| format | Article |
| id | doaj.art-0133fdfef44b489aa0c9bb2e625bb937 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T19:52:02Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0133fdfef44b489aa0c9bb2e625bb9372022-12-21T20:07:57ZengPublic Library of Science (PLoS)PLoS ONE1932-62032021-01-01161e024420210.1371/journal.pone.0244202Revising transcriptome assemblies with phylogenetic information.August GuangMark HowisonFelipe ZapataCharles LawrenceCasey W DunnA common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.https://doi.org/10.1371/journal.pone.0244202 |
| spellingShingle | August Guang Mark Howison Felipe Zapata Charles Lawrence Casey W Dunn Revising transcriptome assemblies with phylogenetic information. PLoS ONE |
| title | Revising transcriptome assemblies with phylogenetic information. |
| title_full | Revising transcriptome assemblies with phylogenetic information. |
| title_fullStr | Revising transcriptome assemblies with phylogenetic information. |
| title_full_unstemmed | Revising transcriptome assemblies with phylogenetic information. |
| title_short | Revising transcriptome assemblies with phylogenetic information. |
| title_sort | revising transcriptome assemblies with phylogenetic information |
| url | https://doi.org/10.1371/journal.pone.0244202 |
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