POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes
Abstract We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05298-w |
| _version_ | 1797836228864770048 |
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| author | Mustafa Siddiqui Gavin C. Conant |
| author_facet | Mustafa Siddiqui Gavin C. Conant |
| author_sort | Mustafa Siddiqui |
| collection | DOAJ |
| description | Abstract We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInTbrowse gives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInTbrowse and the associated data are online at https://wgd.statgen.ncsu.edu . |
| first_indexed | 2024-04-09T15:06:31Z |
| format | Article |
| id | doaj.art-8b1188d5455f45fb9a8f368d8ba6c1af |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T15:06:31Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-8b1188d5455f45fb9a8f368d8ba6c1af2023-04-30T11:30:04ZengBMCBMC Bioinformatics1471-21052023-04-012411810.1186/s12859-023-05298-wPOInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomesMustafa Siddiqui0Gavin C. Conant1Department of Biological Sciences, North Carolina State UniversityDepartment of Biological Sciences, North Carolina State UniversityAbstract We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInTbrowse gives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInTbrowse and the associated data are online at https://wgd.statgen.ncsu.edu .https://doi.org/10.1186/s12859-023-05298-wPOInTComparative genomicsBrowser |
| spellingShingle | Mustafa Siddiqui Gavin C. Conant POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes BMC Bioinformatics POInT Comparative genomics Browser |
| title | POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes |
| title_full | POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes |
| title_fullStr | POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes |
| title_full_unstemmed | POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes |
| title_short | POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes |
| title_sort | pointbrowse orthology prediction and synteny exploration for paleopolyploid genomes |
| topic | POInT Comparative genomics Browser |
| url | https://doi.org/10.1186/s12859-023-05298-w |
| work_keys_str_mv | AT mustafasiddiqui pointbrowseorthologypredictionandsyntenyexplorationforpaleopolyploidgenomes AT gavincconant pointbrowseorthologypredictionandsyntenyexplorationforpaleopolyploidgenomes |