ArticleComputational and structural biotechnology journal2019
MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines.
Article in Computational and structural biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- ZmDLR9 is required for lateral root development via pre-rRNA processing in maize.The Plant journal : for cell and molecular biology · 2026Article
- BbGSD: Black-boned Sheep Genome SNP Database.Database : the journal of biological databases and curation · 2025Article
- A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.BMC biology · 2024Article
- Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis Patient.Current microbiology · 2023Article
- Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture.The Plant cell · 2023Article
- SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics.Computational and structural biotechnology journal · 2023Article
- An adaptive teosinteProceedings of the National Academy of Sciences of the United States of America · 2022Article
- LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.Nucleic acids research · 2022Article
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4 authors.
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Abstract
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.
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