Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies
Daisychain is an interactive graph visualisation and search tool for custom-built gene homology databases. The main goal of Daisychain is to allow researchers working with specific genes to identify homologs in other annotation releases. The gene-centric representation includes local gene neighborho...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-12-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/11/12/2587 |
| _version_ | 1797506998788423680 |
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| author | Oliver Schliebs Chon-Kit Kenneth Chan Philipp E. Bayer Jakob Petereit Ajit Singh Keywan Hassani-Pak Jacqueline Batley David Edwards |
| author_facet | Oliver Schliebs Chon-Kit Kenneth Chan Philipp E. Bayer Jakob Petereit Ajit Singh Keywan Hassani-Pak Jacqueline Batley David Edwards |
| author_sort | Oliver Schliebs |
| collection | DOAJ |
| description | Daisychain is an interactive graph visualisation and search tool for custom-built gene homology databases. The main goal of Daisychain is to allow researchers working with specific genes to identify homologs in other annotation releases. The gene-centric representation includes local gene neighborhood to distinguish orthologs and paralogs by local synteny. The software supports genome sequences in FASTA format and GFF3 formatted annotation files, and the process of building the homology database requires a minimum amount of user interaction. Daisychain includes an integrated web viewer that can be used for both data analysis and data publishing. The web interface extends KnetMaps.js and is based on JavaScript. |
| first_indexed | 2024-03-10T04:40:29Z |
| format | Article |
| id | doaj.art-5c8959b656cd44f6aabfed46acbf1497 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T04:40:29Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-5c8959b656cd44f6aabfed46acbf14972023-11-23T03:24:15ZengMDPI AGAgronomy2073-43952021-12-011112258710.3390/agronomy11122587Daisychain: Search and Interactive Visualisation of Homologs in Genome AssembliesOliver Schliebs0Chon-Kit Kenneth Chan1Philipp E. Bayer2Jakob Petereit3Ajit Singh4Keywan Hassani-Pak5Jacqueline Batley6David Edwards7School of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, AustraliaDepartment of Computational and Analytical Sciences, Rothamsted Research, Harpenden AL5 2JQ, UKDepartment of Computational and Analytical Sciences, Rothamsted Research, Harpenden AL5 2JQ, UKSchool of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, AustraliaDaisychain is an interactive graph visualisation and search tool for custom-built gene homology databases. The main goal of Daisychain is to allow researchers working with specific genes to identify homologs in other annotation releases. The gene-centric representation includes local gene neighborhood to distinguish orthologs and paralogs by local synteny. The software supports genome sequences in FASTA format and GFF3 formatted annotation files, and the process of building the homology database requires a minimum amount of user interaction. Daisychain includes an integrated web viewer that can be used for both data analysis and data publishing. The web interface extends KnetMaps.js and is based on JavaScript.https://www.mdpi.com/2073-4395/11/12/2587comparative genomicscrop genomics<i>Brassica</i> |
| spellingShingle | Oliver Schliebs Chon-Kit Kenneth Chan Philipp E. Bayer Jakob Petereit Ajit Singh Keywan Hassani-Pak Jacqueline Batley David Edwards Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies Agronomy comparative genomics crop genomics <i>Brassica</i> |
| title | Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies |
| title_full | Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies |
| title_fullStr | Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies |
| title_full_unstemmed | Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies |
| title_short | Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies |
| title_sort | daisychain search and interactive visualisation of homologs in genome assemblies |
| topic | comparative genomics crop genomics <i>Brassica</i> |
| url | https://www.mdpi.com/2073-4395/11/12/2587 |
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