MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines
With the rapid decreasing of sequencing cost, large volume of genotype data has been generated in many organisms based on high-throughput sequencing, which was utilized in various fields of biological studies in the post-genome era. The raw sequencing data were usually deposited in the NCBI SRA data...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2019-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037019302478 |
| _version_ | 1818287625707978752 |
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| author | Wei Zhou Lei Wang Wenming Zheng Wen Yao |
| author_facet | Wei Zhou Lei Wang Wenming Zheng Wen Yao |
| author_sort | Wei Zhou |
| collection | DOAJ |
| description | With the rapid decreasing of sequencing cost, large volume of genotype data has been generated in many organisms based on high-throughput sequencing, which was utilized in various fields of biological studies in the post-genome era. The raw sequencing data were usually deposited in the NCBI SRA database. Construction of the database to store and analyze the processed genotype data is an essential step for the utilization of the genotype data by the community. Up to now, a comprehensive genotype database is still missing from maize, which is an important crop of the world. We report the construction of the MaizeSNPDB database using genotype data of 1210 maize line across 35,370,939 SNP sites refined from a large set of genomic variations reported by the maize HapMap 3 project. We further implemented several genetic analysis programs as graphical interfaces in the MaizeSNPDB database. SNPs in user-specified genomic regions could be easily extracted and analyzed in MaizeSNPDB. The whole dataset and code of MaizeSNPDB is available at https://github.com/venyao/MaizeSNPDB. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The MaizeSNPDB database is of great value to future maize functional genomic studies, which can also facilitate marker-assisted breeding in maize. Keywords: Maize, SNP, Database, Genomic variation, Genotype, Graphical interface |
| first_indexed | 2024-12-13T01:43:28Z |
| format | Article |
| id | doaj.art-c261eef2ab9a408ba7cb8ad51df1e612 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-13T01:43:28Z |
| publishDate | 2019-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-c261eef2ab9a408ba7cb8ad51df1e6122022-12-22T00:03:42ZengElsevierComputational and Structural Biotechnology Journal2001-03702019-01-011713771383MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize linesWei Zhou0Lei Wang1Wenming Zheng2Wen Yao3College of Life Sciences, Xinyang Normal University, Xinyang 464000, ChinaNational Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; Corresponding authors.National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; Corresponding authors.With the rapid decreasing of sequencing cost, large volume of genotype data has been generated in many organisms based on high-throughput sequencing, which was utilized in various fields of biological studies in the post-genome era. The raw sequencing data were usually deposited in the NCBI SRA database. Construction of the database to store and analyze the processed genotype data is an essential step for the utilization of the genotype data by the community. Up to now, a comprehensive genotype database is still missing from maize, which is an important crop of the world. We report the construction of the MaizeSNPDB database using genotype data of 1210 maize line across 35,370,939 SNP sites refined from a large set of genomic variations reported by the maize HapMap 3 project. We further implemented several genetic analysis programs as graphical interfaces in the MaizeSNPDB database. SNPs in user-specified genomic regions could be easily extracted and analyzed in MaizeSNPDB. The whole dataset and code of MaizeSNPDB is available at https://github.com/venyao/MaizeSNPDB. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The MaizeSNPDB database is of great value to future maize functional genomic studies, which can also facilitate marker-assisted breeding in maize. Keywords: Maize, SNP, Database, Genomic variation, Genotype, Graphical interfacehttp://www.sciencedirect.com/science/article/pii/S2001037019302478 |
| spellingShingle | Wei Zhou Lei Wang Wenming Zheng Wen Yao MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines Computational and Structural Biotechnology Journal |
| title | MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines |
| title_full | MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines |
| title_fullStr | MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines |
| title_full_unstemmed | MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines |
| title_short | MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines |
| title_sort | maizesnpdb a comprehensive database for efficient retrieve and analysis of snps among 1210 maize lines |
| url | http://www.sciencedirect.com/science/article/pii/S2001037019302478 |
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