The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

2012 | Philippe Lamesch, Tanya Z. Berardini, Donghui Li, David Swarbreck, Christopher Wilks, Rajkumar Sasidharan, Robert Muller, Kate Dreher, Debbie L. Alexander, Margarita Garcia-Hernandez, Athikkattuvavalu S. Karthikeyan, Cynthia H. Lee, William D. Nelson, Larry Ploetz, Shanker Singh, April Wensel and Eva Huala
The Arabidopsis Information Resource (TAIR) is a comprehensive database for Arabidopsis thaliana, providing gene function annotations, genome assemblies, and a variety of tools for researchers. Recent updates include new genome releases (TAIR8, TAIR9, TAIR10), which improved gene annotations, re-annotated pseudogenes and transposon genes, and incorporated new data from proteomics and transcriptomics. TAIR also introduced Textpresso for full-text literature searches and enhanced functional annotation tools. The database includes genomic sequences, gene structures, metabolic pathways, gene expression data, and community-submitted annotations. TAIR's gene function annotations use Gene Ontology (GO) and Plant Ontology (PO) terms, with computational methods used to assign GO terms based on protein domains and sequence similarity. TAIR's genome annotation team has continuously improved the A. thaliana genome annotation, with TAIR10 incorporating RNA-seq data and new proteome data. The TAIR10 release includes 126 new genes and 2099 new splice variants, with 95.7% of protein-coding genes having partial transcript support. TAIR provides various tools for genome browsing, including GBrowse_syn for synteny analysis and the Integrated Genome Browser (IGB) for visualizing large-scale datasets. TAIR also maintains AraCyc, a resource for Arabidopsis metabolic pathways and enzymes. The database is widely used by the plant biology community, with over 22,000 registered users. TAIR continues to expand its resources and tools to support research on Arabidopsis and other plant species.The Arabidopsis Information Resource (TAIR) is a comprehensive database for Arabidopsis thaliana, providing gene function annotations, genome assemblies, and a variety of tools for researchers. Recent updates include new genome releases (TAIR8, TAIR9, TAIR10), which improved gene annotations, re-annotated pseudogenes and transposon genes, and incorporated new data from proteomics and transcriptomics. TAIR also introduced Textpresso for full-text literature searches and enhanced functional annotation tools. The database includes genomic sequences, gene structures, metabolic pathways, gene expression data, and community-submitted annotations. TAIR's gene function annotations use Gene Ontology (GO) and Plant Ontology (PO) terms, with computational methods used to assign GO terms based on protein domains and sequence similarity. TAIR's genome annotation team has continuously improved the A. thaliana genome annotation, with TAIR10 incorporating RNA-seq data and new proteome data. The TAIR10 release includes 126 new genes and 2099 new splice variants, with 95.7% of protein-coding genes having partial transcript support. TAIR provides various tools for genome browsing, including GBrowse_syn for synteny analysis and the Integrated Genome Browser (IGB) for visualizing large-scale datasets. TAIR also maintains AraCyc, a resource for Arabidopsis metabolic pathways and enzymes. The database is widely used by the plant biology community, with over 22,000 registered users. TAIR continues to expand its resources and tools to support research on Arabidopsis and other plant species.
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