EASED: Extended alternatively spliced EST database
EASED: Extended alternatively spliced EST database
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DOI：
10.1093/nar/gkh136
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Reich, JG
中科院分区：
文献类型：
--
作者：
Pospisil, H;Herrmann, A;Reich, JG
我们建立了一个数据库的选择性剪接形式（ASforms）的9种真核生物。AS型通过使用BLAST比较高分EST与mRNA序列来定义，采用已知的外显子-内含子信息（来自Ensembi数据库）。过滤程序比较每个比对序列对的末端在EST序列中的缺失或插入，这表明相对于外显子-内含子边界存在选择性剪接形式。此外，我们定义了每个人类序列的选择性剪接模式。它表示每个mRNA中选择性剪接的EST（NAE）的数量、组成性剪接的EST（NCE）的数量以及选择性剪接位点（NSS）的数量。NAE和NCE对应于EST覆盖率，可以用作预测可变剪接变体的质量指标。NSS值指定基因的剪接倾向。此外，还包括所有EST的组织类型信息。这允许（i）将搜索限制在某些组织，以及（iii）计算组织-NAE、组织-NCE和组织-NSS。这些评分适用于估计某些AS型的组织特异性。此外，还可以获得EST的发育阶段和疾病信息。EASED可在http：eased.bioinf.mdc-berlin.de/上访问。
We established a database of alternative splice forms (ASforms) for nine eukaryotic organisms. ASforms are defined by comparing high-scoring ESTs with mRNA sequences using BLAST, taking known exon-intron information (from the Ensembi database). Filtering programs compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which indicate the existence of alternative splice forms with respect to the exon-intron boundaries. Moreover, we defined the alternative splice profile of each human sequence. It indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE correspond to the EST coverage and can be used as a quality indicator for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene. Additionally, the tissue type information of all ESTs was included. This allows (i) restriction of the search to certain tissues and (iii) calculation of the tissue-NAEs, tissue-NCEs and tissue-NSS. These scores are suitable for the estimation of tissue specificity of certain ASforms. Furthermore, the developmental stage and disease information of the ESTs is available. EASED is accessible at http: eased.bioinf.mdc-berlin.de/.