BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions
The rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and great opportunities for researchers to investigate genomic variations across hundreds or even thousands of accessions in the post-genomic era. The management and explora...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037020304153 |
| _version_ | 1818452332094947328 |
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| author | Tao Yan Qian Wang Antony Maodzeka Dezhi Wu Lixi Jiang |
| author_facet | Tao Yan Qian Wang Antony Maodzeka Dezhi Wu Lixi Jiang |
| author_sort | Tao Yan |
| collection | DOAJ |
| description | The rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and great opportunities for researchers to investigate genomic variations across hundreds or even thousands of accessions in the post-genomic era. The management and exploration of these large-scale genomic variations heavily rely on programming and command-line environments, which are challenging and time-consuming for most experimental biologists and plant breeders. Here, we present BnaSNPDB, an interactive web portal with a user-friendly interface that provides multiple analysis modules for retrieving, analyzing, and visualizing single nucleotide polymorphisms among 1,007 accessions of worldwide rapeseed germplasm. It is compatible, extendable, and portable to be easily set up on different operating systems, and can be accessed at http://121.41.229.126:3838/bnasnpdb and http://rapeseed.zju.edu.cn:3838/bnasnpdb. Its whole dataset and code are available at https://github.com/YTLogos/BnaSNPDB. This database is essential for accelerating studies on the functional genomics and screening of the molecular markers of molecular-assisted breeding in rapeseed. |
| first_indexed | 2024-12-14T21:21:24Z |
| format | Article |
| id | doaj.art-0791a148dc414fd39b89518d08c211d0 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-14T21:21:24Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-0791a148dc414fd39b89518d08c211d02022-12-21T22:46:56ZengElsevierComputational and Structural Biotechnology Journal2001-03702020-01-011827662773BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessionsTao Yan0Qian Wang1Antony Maodzeka2Dezhi Wu3Lixi Jiang4Provincial Key Laboratory of Crop Gene Resource, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou 310058, PR ChinaProvincial Key Laboratory of Crop Gene Resource, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou 310058, PR ChinaProvincial Key Laboratory of Crop Gene Resource, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou 310058, PR ChinaProvincial Key Laboratory of Crop Gene Resource, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou 310058, PR ChinaCorresponding author.; Provincial Key Laboratory of Crop Gene Resource, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou 310058, PR ChinaThe rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and great opportunities for researchers to investigate genomic variations across hundreds or even thousands of accessions in the post-genomic era. The management and exploration of these large-scale genomic variations heavily rely on programming and command-line environments, which are challenging and time-consuming for most experimental biologists and plant breeders. Here, we present BnaSNPDB, an interactive web portal with a user-friendly interface that provides multiple analysis modules for retrieving, analyzing, and visualizing single nucleotide polymorphisms among 1,007 accessions of worldwide rapeseed germplasm. It is compatible, extendable, and portable to be easily set up on different operating systems, and can be accessed at http://121.41.229.126:3838/bnasnpdb and http://rapeseed.zju.edu.cn:3838/bnasnpdb. Its whole dataset and code are available at https://github.com/YTLogos/BnaSNPDB. This database is essential for accelerating studies on the functional genomics and screening of the molecular markers of molecular-assisted breeding in rapeseed.http://www.sciencedirect.com/science/article/pii/S2001037020304153SNPDatabaseRapeseedGenomic variation |
| spellingShingle | Tao Yan Qian Wang Antony Maodzeka Dezhi Wu Lixi Jiang BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions Computational and Structural Biotechnology Journal SNP Database Rapeseed Genomic variation |
| title | BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions |
| title_full | BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions |
| title_fullStr | BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions |
| title_full_unstemmed | BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions |
| title_short | BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions |
| title_sort | bnasnpdb an interactive web portal for the efficient retrieval and analysis of snps among 1 007 rapeseed accessions |
| topic | SNP Database Rapeseed Genomic variation |
| url | http://www.sciencedirect.com/science/article/pii/S2001037020304153 |
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