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Scripting Analyses of Genomes in Ensembl Plants
Ensembl Plants ( http://plants.ensembl.org ) offers genome-scale information for plants, with four releases...
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RETRACTED ARTICLE: BCLncRDB: a comprehensive database of LncRNAs associated with breast cancer
Breast cancer, the most common cancer in women, is characterized by high morbidity and mortality worldwide. Recent evidence has shown that long...
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Wheat Data Integration and FAIRification: IWGSC, GrainGenes, Ensembl and Other Data Repositories
Wheat data integration and FAIRification are key to tackling the challenge of wheat improvement. The data repositories presented in this chapter play...
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DSP: database of disease susceptibility genes in plants
Host-pathogen interaction is the most crucial factor that evokes the host immune system to fight against pathogens. In contrast to specialized immune...
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SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis
BackgroundCurrent proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus,...
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Exploring microproteins from various model organisms using the mip-mining database
Microproteins, prevalent across all kingdoms of life, play a crucial role in cell physiology and human health. Although global gene transcription is...
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AtlasGrabber: a software facilitating the high throughput analysis of the human protein atlas online database
BackgroundThe human protein atlas (HPA) is an online database containing large sets of protein expression data in normal and cancerous tissues in...
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CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)
BackgroundThe domestic dog, Canis lupus familiaris , is a companion animal for humans as well as an animal model in cancer research due to similar...
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BGFD: an integrated multi-omics database of barley gene families
BackgroundA gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and...
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WeCoNET: a host–pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms
BackgroundTriticum aestivum is the most important staple food grain of the world. In recent years, the outbreak of a major seed-borne disease,...
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A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals
BackgroundLivestock animals is of great significance in agricultural production. However, the role of specific gene expression, especially...
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Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools
BackgroundChinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological...
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Canis MitoSNP database: a functional tool useful for comparative analyses of human and canine mitochondrial genomes
Canis MitoSNP is a tool allowing assignment of each mitochondrial genomic position a corresponding position in the mitochondrial gene and in the...
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AgroLD: A Knowledge Graph Database for Plant Functional Genomics
Recent advances in high-throughput technologies have resulted in tremendous increase in the amount of data in the agronomic domain. There is an...
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The VGNC: expanding standardized vertebrate gene nomenclature
The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclature Committee, to approve...
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GenArk: towards a million UCSC genome browsers
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome...
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Impact of gene annotation choice on the quantification of RNA-seq data
BackgroundRNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression...
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MoG+: a database of genomic variations across three mouse subspecies for biomedical research
Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic...
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AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite...
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Database Resources for Functional Circular RNAs
Circular RNA (or circRNA) is a type of single-stranded covalently closed circular RNA molecule and play important roles in diverse biological...