ArticleNucleic acids research2020
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- ALGI: Sparse Convolutional Denoising Autoencoder Utilizing Local Genomic Information for Genotype Imputation.Animals : an open access journal from MDPI · 2026Article
- Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Advancements in Animal Breeding: From Mendelian Genetics to Machine Learning.International journal of molecular sciences · 2025Review
- A comprehensive genome-wide analysis for signatures of selection in goat (genus Capra) revealed new candidate genes for environmental adaptation and productive traits.BMC genomics · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs.Nature communications · 2024Article
- Introgression drives adaptation to the plateau environment in a subterranean rodent.BMC biology · 2024Article
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets.BMC genomic data · 2024Article
- AGIDB: a versatile database for genotype imputation and variant decoding across species.Nucleic acids research · 2024Article
- RNA-Seq based selection signature analysis for identifying genomic footprints associated with the fat-tail phenotype in sheep.Frontiers in veterinary science · 2024Article
- Vet informatics and the future of drug discovery in veterinary medicine.Frontiers in veterinary science · 2024Article
- Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences.Nature communications · 2023Article
- The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs.Communications biology · 2023Article
- The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle.Genetics, selection, evolution : GSE · 2023Article
- Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs.Journal of animal science and biotechnology · 2023Article
- GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals.Nucleic acids research · 2023Article
- IAnimal: a cross-species omics knowledgebase for animals.Nucleic acids research · 2023Article
- PHARP: a pig haplotype reference panel for genotype imputation.Scientific reports · 2022Article
- Animal-eRNAdb: a comprehensive animal enhancer RNA database.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs) and thus can be widely used in large-scale genome-wide association studies (GWASs) using relatively inexpensive and low-density SNP arrays. However, most animals except humans lack high-quality reference panels, which greatly limits the application of genotype imputation in animals. To overcome this limitation, we developed Animal-ImputeDB, which is dedicated to collecting genotype data and whole-genome resequencing data of nonhuman animals from various studies and databases. A computational pipeline was developed to process different types of raw data to construct reference panels. Finally, 13 high-quality reference panels including ∼400 million SNPs from 2265 samples were constructed. In Animal-ImputeDB, an easy-to-use online tool consisting of two popular imputation tools was designed for the purpose of genotype imputation. Collectively, Animal-ImputeDB serves as an important resource for animal genotype imputation and will greatly facilitate research on animal genomic selection and genetic improvement.
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Registered trials
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