DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements.
DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements.
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DEG 10，必需基因数据库的更新，包括蛋白质编码基因和非编码基因组元件
DOI：
10.1093/nar/gkt1131
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发表时间：
2014-01
影响因子：
14.9
通讯作者：
Zhang R
中科院分区：
文献类型：
--
作者：
Luo H;Lin Y;Gao F;Zhang CT;Zhang R
高密度转座子介导的诱变与高通量测序相结合，在必需基因的研究方面取得了重大进展，使得在不同条件下已鉴定的原核生物必需基因数量大幅增加，并且修正了必需基因的概念，即包括所有必需的基因组元件，而不仅仅关注蛋白质编码基因。必需基因数据库（DEG）的新版本DEG 10（可在http://www.essentialgene.org获取）已开发出来，以适应这些数量和质量上的进步。除了增加通过全基因组基因必需性筛选确定的细菌和古菌必需基因数量外，DEG 10还包含必需的非编码RNA、启动子、调控序列和复制起点。这些必需的基因组元件不仅在体外确定，而且在包括生存、致病和抗生素抗性等不同条件下的体内确定。我们开发了可定制的BLAST工具，允许用户针对单个基因、基因列表、有注释或无注释的基因组进行特定物种和特定实验的BLAST搜索。因此，DEG 10包含了生命三个域中不同条件下的必需基因组元件，并带有可定制的BLAST工具。
The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. DEG 10, a new release of the Database of Essential Genes (available at http://www.essentialgene.org), has been developed to accommodate these quantitative and qualitative advancements. In addition to increasing the number of bacterial and archaeal essential genes determined by genome-wide gene essentiality screens, DEG 10 also harbors essential noncoding RNAs, promoters, regulatory sequences and replication origins. These essential genomic elements are determined not only in vitro, but also in vivo, under diverse conditions including those for survival, pathogenesis and antibiotic resistance. We have developed customizable BLAST tools that allow users to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annotated or unannotated genomes. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.
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影响因子：
9.9
作者：
通讯作者：
--
影响因子：
9.9
作者：
de Berardinis, Veronique;Vallenet, David;Castelli, Vanina;Besnard, Marielle;Pinet, Agnes;Cruaud, Corinne;Samair, Sumitta;Lechaplais, Christophe;Gyapay, Gabor;Richez, Celine;Durot, Maxime;Kreimeyer, Annett;Le Fevre, Francois;Schaechter, Vincent;Pezo, Valerie;Doering, Volker;Scarpelli, Claude;Medigue, Claudine;Cohen, Georges N.;Marliere, Philippe;Salanoubat, Marcel;Weissenbach, Jean
通讯作者：
Weissenbach, Jean
影响因子：
14.9
作者：
Chen WH;Minguez P;Lercher MJ;Bork P
通讯作者：
Bork P
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
4.4
作者：
Chaudhuri RR;Allen AG;Owen PJ;Shalom G;Stone K;Harrison M;Burgis TA;Lockyer M;Garcia-Lara J;Foster SJ;Pleasance SJ;Peters SE;Maskell DJ;Charles IG
通讯作者：
Charles IG