EID: the Exon-Intron Database - an exhaustive database of protein-coding intron-containing genes
EID: the Exon-Intron Database - an exhaustive database of protein-coding intron-containing genes
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DOI：
10.1093/nar/28.1.185
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发表时间：
2000-01-01
影响因子：
14.9
通讯作者：
Gilbert, W
中科院分区：
文献类型：
--
作者：
Saxonov, S;Daizadeh, I;Gilbert, W
为了帮助分子进化研究和基因预测研究，我们构建了FASTA格式的外显子-内含子数据库（EID）。目前，该数据库来源于GenBank第112版，它包含51 289个蛋白质编码基因（287 209个外显子），其中包含内含子，以及每个基因及其DNA和蛋白质序列的广泛描述，以及剪接基序信息。从基因库继承了17%的冗余，在99%的身份水平上进行清除，将数据库减少到42 460个基因（243 589个外显子）。我们已经创建了基因亚数据库，这些基因的内含子位置已经通过实验确定。其中一个数据库是通过比较基因组序列和mRNA序列构建的，包含11 242个基因（62 474个外显子）。通过选择关键词剔除计算机预测基因，构建了包含22 196个基因（105 595个外显子）的数据库。通过检查与内含子边界相邻的两个核苷酸，我们推断与标准GT存在2%的错误率或其他偏差。核基因中的AG基序。该准则可用于从整个数据库中剔除4921个基因。提供了各种工具来生成用户特定的EID子集。EID分布可从http:/mcb.harvard.edu/gilbert/EID获取。
To aid studies of molecular evolution and to assist in gene prediction research, we have constructed an Exon-Intron Database (EID) in FASTA format. Currently, the database is derived from GenBank release 112, and it contains 51 289 protein-coding genes (287 209 exons) that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. There is 17% redundancy inherited from GenBank-a purge at the 99% identity level reduced the data-base to 42 460 genes (243 589 exons). We have created subdatabases of genes whose intron positions have been experimentally determined. One such database, constructed by comparing genomic and mRNA sequences, contains 11 242 genes (62 474 exons). A larger database of 22 196 genes (105 595 exons) was constructed by selecting on keywords to eliminate computer-predicted genes. By examining the two nucleotides adjacent to the intron boundary, we infer that there is a 2% rate of errors or other deviations from the standard GT...AG motif in nuclear genes. This criterion can be used to eliminate 4921 genes from the overall database. Various tools are provided to enable generation of user-specific subsets of the EID. The EID distribution can be obtained from http:/mcb.harvard.edu/gilbert/EID.