Joint IRB-BSC program on Computational Biology, BSC c/ Jordi Girona 29, Catalonia.
Bioinformatics. 2012 Mar 15;28(6):763-70. doi: 10.1093/bioinformatics/bts024. Epub 2012 Jan 16.
The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.
We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith-Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.
基因表达相关基因组区域的预测和注释在很大程度上已经得到了探索。大部分的精力都集中在开发检测转录起始位点的方法上，而识别调控区域及其功能转录因子结合位点（TFBS）的方法在很大程度上仍未得到探索，并且存在重要的定量和定性方法上的差距。
我们开发了 ReLA（用于调控区域局部比对的工具），这是一种独特的工具，使用 Smith-Waterman 算法进行了优化，可以进行保守 TFBS 簇的局部搜索，并检测基因和增强子区域附近的调控区域。当在实验验证的近端调控区域和增强子上进行测试时，ReLA 的性能分别显示出 81%和 50%的特异性。
