Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining with Specific Numbers of Gaps

Yu Hao Ke, Jen Wei Huang, Wei Chen Lin, Bijay Prasad Jaysawal

研究成果: Article同行評審

5 引文 斯高帕斯(Scopus)

摘要

Identifying motifs in promoter regions is crucial to our understanding of transcription regulation. Researchers commonly use known promoter features in a variety of species to predict promoter motifs. However the results are not particularly useful. Different species rarely have similar features in promoter binding sites. In this study, we adopt sequence analysis techniques to find the possible promoter binding sites among different species. We sought to improve the existing algorithm to suit the task of mining sequential patterns with specific number of gaps. Moreover, we discuss the implementation of proposed method in a distributed environment. The proposed method finds the transcription start sites (TSS) and extracts possible promoter regions from DNA sequences according to TSS. We derived the motifs in the possible promoter regions, while taking into account the number of gaps in the motifs to deal with unimportant nucleotides. The motifs generated from promoter regions using the proposed methodology were shown to tolerate unimportant nucleotides. A comparison with known promoter motifs verified the efficacy of the proposed method.

原文English
頁(從 - 到)2459-2470
頁數12
期刊IEEE/ACM Transactions on Computational Biology and Bioinformatics
18
發行號6
DOIs
出版狀態Published - 2021

All Science Journal Classification (ASJC) codes

  • 生物技術
  • 遺傳學
  • 應用數學

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