Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.
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DOI：
10.1093/nar/gki045
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Hardison RC
中科院分区：
文献类型：
--
作者：
Elnitski L;Giardine B;Shah P;Zhang Y;Riemer C;Weirauch M;Burhans R;Miller W;Hardison RC
我们描述了两个数据库的改进，使访问信息的基因组序列的相似性，DNA中的功能元件和实验结果，证明这些功能。GALA，基因组比对和注释数据库，现在是一套相互关联的关系数据库，为五个脊椎动物物种，人类，黑猩猩，小鼠，大鼠和鸡。对于每个物种，GALA记录成对和多个序列比对，从这些比对中得出的分数反映了在纯化选择下或作为调节元件的可能性，以及广泛的注释，如基因，基因表达模式和转录因子结合位点。用户界面支持简单和复杂的查询，包括减法和交集等操作，以及聚类和查找要素附近的元素。dbERGE II，基因表达实验结果数据库，包含来自各种功能测定的实验数据。这两个数据库现在都在DB2数据库管理系统上运行。改进的硬件和调优减少了响应时间并增加了查询容量，而简化的查询界面将有助于指导新用户完成查询过程。链接可在http://www.bx.psu.edu/上找到。
We describe improvements to two databases that give access to information on genomic sequence similarities, functional elements in DNA and experimental results that demonstrate those functions. GALA, the database of Genome ALignments and Annotations, is now a set of interlinked relational databases for five vertebrate species, human, chimpanzee, mouse, rat and chicken. For each species, GALA records pairwise and multiple sequence alignments, scores derived from those alignments that reflect the likelihood of being under purifying selection or being a regulatory element, and extensive annotations such as genes, gene expression patterns and transcription factor binding sites. The user interface supports simple and complex queries, including operations such as subtraction and intersections as well as clustering and finding elements in proximity to features. dbERGE II, the database of Experimental Results on Gene Expression, contains experimental data from a variety of functional assays. Both databases are now run on the DB2 database management system. Improved hardware and tuning has reduced response times and increased querying capacity, while simplified query interfaces will help direct new users through the querying process. Links are available at http://www.bx.psu.edu/.
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影响因子：
64.5
作者：
Cawley, S;Bekiranov, S;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
14.9
作者：
Wheeler DL;Church DM;Edgar R;Federhen S;Helmberg W;Madden TL;Pontius JU;Schuler GD;Schriml LM;Sequeira E;Suzek TO;Tatusova TA;Wagner L
通讯作者：
Wagner L
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
影响因子：
7
作者：
Giardine, B;Elnitski, L;Hardison, RC
通讯作者：
Hardison, RC
影响因子：
7
作者：
Ovcharenko, I;Loots, GG;Stubbs, L
通讯作者：
Stubbs, L