ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.
ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.
复制标题
Probealign：将基于高通量测序的结构探测信息纳入NCRNA同源性搜索。
DOI：
10.1186/1471-2105-15-s9-s15
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发表时间：
2014
影响因子：
3
通讯作者：
Zhang S
中科院分区：
文献类型：
--
作者：
Ge P;Zhong C;Zhang S
RNA结构探测技术的最新进展，包括基于高通量测序的技术，提高了热力学折叠的准确性与定量核苷酸分辨率的结构信息。在本文中，我们提出了一种新的方法，ProbeAlign，将高通量RNA结构探测的反应性纳入ncRNA同源性搜索的功能注释。为了减少大规模数据结构对齐的开销，查询序列中的特定配对模式被忽略。另一方面，检索嵌入在探测数据中的靶序列的部分结构信息以指导比对。因此，结构比对问题转化为一个序列比对问题与额外的反应性信息。基准测试结果表明，ProbeAlign的预测精度优于基于滤波的CMsearch，计算效率高。ProbeAlign对FragSeq数据的应用（基于全基因组结构探测）已经证明了其在高通量测序的大规模数据集中搜索ncRNA的能力。通过结合高通量测序的结构探测信息，ProbeAlign可以提高ncRNA同源性搜索的准确性和效率。这是一个很有前途的工具，ncRNA功能注释的全基因组数据集。ProbeAlign的源代码可在http://genome.ucf.edu/ProbeAlign上获得。
Recent advances in RNA structure probing technologies, including the ones based on high-throughput sequencing, have improved the accuracy of thermodynamic folding with quantitative nucleotide-resolution structural information. In this paper, we present a novel approach, ProbeAlign, to incorporate the reactivities from high-throughput RNA structure probing into ncRNA homology search for functional annotation. To reduce the overhead of structure alignment on large-scale data, the specific pairing patterns in the query sequences are ignored. On the other hand, the partial structural information of the target sequences embedded in probing data is retrieved to guide the alignment. Thus the structure alignment problem is transformed into a sequence alignment problem with additional reactivity information. The benchmark results show that the prediction accuracy of ProbeAlign outperforms filter-based CMsearch with high computational efficiency. The application of ProbeAlign to the FragSeq data, which is based on genome-wide structure probing, has demonstrated its capability to search ncRNAs in a large-scale dataset from high-throughput sequencing. By incorporating high-throughput sequencing-based structure probing information, ProbeAlign can improve the accuracy and efficiency of ncRNA homology search. It is a promising tool for ncRNA functional annotation on genome-wide datasets. The source code of ProbeAlign is available at http://genome.ucf.edu/ProbeAlign.