Huang Y-H, Chen Y-T, Lai J-J, Yang S-T, Yang U-C
Bioinformatics Program, National Yang-Ming University, No. 155, Sec. 2, Li-Noun Street, Taipei, Taiwan 11221, Republic of China.
Nucleic Acids Res. 2002 Jan 1;30(1):186-90. doi: 10.1093/nar/30.1.186.
PALS db is a collection of Putative Alternative Splicing information from 19 936 human UniGene clusters and 16 615 mouse UniGene clusters. Alternative splicing (AS) sites were predicted by using the longest messenger RNA (mRNA) sequence in each UniGene cluster as the reference sequence. This sequence was aligned with related sequences in UniGene and dbEST to reveal the AS. This information was presented with six features: (i) literature aliases were used to improve the result of a gene name search; (ii) the quality of a prediction can be easily judged from the color-coded similarity and the scaled length of an alignment; (iii) we have clustered those EST sequences that support the same AS site together to enhance the users' confidence on a prediction; (iv) the users can also set up the alignment criteria interactively to recover false negatives; (v) tissue distribution can be displayed by placing the mouse cursor over an alignment; (vi) gene features will be analyzed at foreign sites by submitting the selected mRNA or its encoded protein as a query. Using these features, the users cannot only discover putative AS sites in silico, but also make new observations by combining AS information with tissue distributions or with gene features. PALS db is available at http://palsdb.ym.edu.tw/.
PALS数据库收集了来自19936个人类单基因簇和16615个小鼠单基因簇的假定可变剪接信息。可变剪接（AS）位点是通过将每个单基因簇中最长的信使核糖核酸（mRNA）序列作为参考序列来预测的。该序列与单基因簇和dbEST中的相关序列进行比对以揭示可变剪接。这些信息以六个特征呈现：（i）使用文献别名来改进基因名称搜索结果；（ii）可根据颜色编码的相似性和比对的缩放长度轻松判断预测质量；（iii）我们将支持相同AS位点的那些EST序列聚类在一起，以增强用户对预测的信心；（iv）用户还可以交互式设置比对标准以找回假阴性；（v）将鼠标光标悬停在比对上可显示组织分布；（vi）通过提交所选mRNA或其编码蛋白作为查询，将在外部位点分析基因特征。利用这些特征，用户不仅可以在计算机上发现假定的AS位点，还可以通过将AS信息与组织分布或基因特征相结合来做出新的观察。PALS数据库可在http://palsdb.ym.edu.tw/获取。
