The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.
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DOI：
10.1093/nar/gkt1029
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发表时间：
2014-01
影响因子：
14.9
通讯作者：
Wortman JR
中科院分区：
文献类型：
--
作者：
Cerqueira GC;Arnaud MB;Inglis DO;Skrzypek MS;Binkley G;Simison M;Miyasato SR;Binkley J;Orvis J;Shah P;Wymore F;Sherlock G;Wortman JR
曲霉基因组数据库（AspGD；http://www.aspgd.org）是一个免费的网络资源，专为曲霉研究人员设计，也是整个真菌研究界的宝贵信息来源。除了作为基因组、转录组和多态性数据的存储库和访问中心点之外，AspGD 还拥有一个全面的比较基因组学工具箱，有助于在 20 个当前可用的曲霉属基因组中探索预先计算的直系同源物。 AspGD 管理者根据四种主要曲霉属物种的文献综述进行基因产物注释：构巢曲霉、米曲霉、烟曲霉和黑曲霉。我们通过分析公开的转录数据（主要是表达的测序标签）迭代地改进了曲霉基因组的结构注释，如之前的 NAR 数据库文章（Arnaud 等人，2012）中所述。在此更新中，我们根据最近可用的 RNA-Seq 数据报告了构巢曲霉、米曲霉和烟曲霉基因组的实质性结构注释改进。这些物种中超过 26,000 个基因座得到更新；尽管这些主要包括非翻译区 (UTR) 的添加和延伸，但新的分析还实现了 1000 多个影响每个目标基因组中基因编码序列的修改。
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community. In addition to being a repository and central point of access to genome, transcriptome and polymorphism data, AspGD hosts a comprehensive comparative genomics toolbox that facilitates the exploration of precomputed orthologs among the 20 currently available Aspergillus genomes. AspGD curators perform gene product annotation based on review of the literature for four key Aspergillus species: Aspergillus nidulans, Aspergillus oryzae, Aspergillus fumigatus and Aspergillus niger. We have iteratively improved the structural annotation of Aspergillus genomes through the analysis of publicly available transcription data, mostly expressed sequenced tags, as described in a previous NAR Database article (Arnaud et al. 2012). In this update, we report substantive structural annotation improvements for A. nidulans, A. oryzae and A. fumigatus genomes based on recently available RNA-Seq data. Over 26 000 loci were updated across these species; although those primarily comprise the addition and extension of untranslated regions (UTRs), the new analysis also enabled over 1000 modifications affecting the coding sequence of genes in each target genome.
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影响因子：
14.9
作者：
Hunter S;Jones P;Mitchell A;Apweiler R;Attwood TK;Bateman A;Bernard T;Binns D;Bork P;Burge S;de Castro E;Coggill P;Corbett M;Das U;Daugherty L;Duquenne L;Finn RD;Fraser M;Gough J;Haft D;Hulo N;Kahn D;Kelly E;Letunic I;Lonsdale D;Lopez R;Madera M;Maslen J;McAnulla C;McDowall J;McMenamin C;Mi H;Mutowo-Muellenet P;Mulder N;Natale D;Orengo C;Pesseat S;Punta M;Quinn AF;Rivoire C;Sangrador-Vegas A;Selengut JD;Sigrist CJ;Scheremetjew M;Tate J;Thimmajanarthanan M;Thomas PD;Wu CH;Yeats C;Yong SY
通讯作者：
Yong SY
影响因子：
7
作者：
Skinner, Mitchell E.;Uzilov, Andrew V.;Holmes, Ian H.
通讯作者：
Holmes, Ian H.
影响因子：
5.8
作者：
Riley, David R.;Angiuoli, Samuel V.;Tettelin, Herve
通讯作者：
Tettelin, Herve
影响因子：
7
作者：
Andersen, Mikael R.;Salazar, Margarita P.;Baker, Scott E.
通讯作者：
Baker, Scott E.
影响因子：
14.9
作者：
Haas, BJ;Delcher, AL;White, O
通讯作者：
White, O