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WheatGene: A genomics database for common wheat and its related species 被引量:1
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作者 Diego F.Garcia Zhengyu Wang +4 位作者 Jiantao Guan Lingjie Yin Shuaifeng Geng Aili Li Long Mao 《The Crop Journal》 SCIE CSCD 2021年第6期1486-1491,共6页
Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology ... Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org. 展开更多
关键词 WHEAT genome Comparative genomics DATABASE genome browser
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3D Genome Tuner:Compare Multiple Circular Genomes in a 3D Context
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作者 Qi Wang Qun Liang Xiuqing Zhang 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2009年第3期143-146,共4页
Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not off... Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner,a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. The program is freely available (under an LGPL licence) at http://sourceforge.net/projects/dgenometuner. 展开更多
关键词 three dimensional circular map genome browser comparative genomics
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