Development and maintenance of bioinformatics tools for mouse biology

在我们之前的工作中，我们开发了四个主要的生物信息学工具/数据库：(1)基于Web的ANOVA-FDR软件，用于提供用户友好的微阵列数据分析(http://lgsun.grc.nia.nih.gov/ANOVA/)；)；(2)用于从与小鼠基因组比对的表达序列进行转录组装的算法和全自动计算流水线；(3)基于Web的浏览器，用于可视化所有转录本和小鼠基因的替代剪接形式(NIA小鼠基因索引：http://lgsun.grc.nia.nih.gov/geneindex/mm9/)；(4)基于网络的数据库和工具，用于可视化和绘制小鼠基因组的转录因子结合位点(Cisview：http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html)；)和(5)基于全基因组染色质免疫沉淀结合测序(CHIP-SEQ)方法的基于网络的工具(Cisfinder：http：http://lgsun.grc.nia.nih.gov/CisFinder/).在过去的一年里，我们一直致力于维护和更新这些生物信息学资源。我们还开发了一种新的算法来模拟两个相互竞争的转录因子调控的基因表达。

In our previous work, we developed four major bioinformatics tools/databases: (1) the web-based ANOVA-FDR software to provide user-friendly microarray data analysis (http://lgsun.grc.nia.nih.gov/ANOVA/); (2) an algorithm and a fully-automated computational pipeline for transcript assembly from expressed sequences aligned to the mouse genome; (3) a web-based browser to visualize all transcripts and alternative spliced forms of mouse genes (NIA Mouse Gene Index: http://lgsun.grc.nia.nih.gov/geneindex/mm9/); (4) a web-based database and tool to visualize and map the transcription factor binding sites of the mouse genome (CisView: http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html); and (5) a web-based tool to identify consensus sequence motifs based on the genome-wide chromatin-immunoprecipitation coupled with sequencing (ChIP-Seq) method (CisFinder: http: http://lgsun.grc.nia.nih.gov/CisFinder/). During the last year, we have been working on maintaining and updating these bioinformatics resources. We have also developed a new algorithm to simulate the gene expression regulated by two competing transcription factors.