Interactive Sequencing by Hybridization

本项目探索了一种新的杂交测序方法(SBH)，该方法利用相互作用大大减少了大DNA片段从头测序所需的寡核苷酸数量，同时保留了SBH的主要优势--并行性。该项目的目标包括：(1)开发用于测序芯片交互设计的高效算法；以及(2)利用模拟结果来确定64kb片段可以被测序(使用大约十轮标准大小的64k寡核苷酸阵列获得)。该项目包括以下交互式SBH的理论和实验室研究：(A)与英国牛津大学的生物化学家合作，研究了在各种制造技术下设计和制造SBH阵列的算法问题；(B)研究了在非经典芯片设计和杂交错误等复杂情况下根据杂交数据重建DNA序列所固有的算法问题；以及(C)研究了SBH的其他新型变体所固有的算法问题，特别是基于光刻的交互式SBH和定位SBH。该项目与计算生物学活动联合资助。*

This project explores a new approach to sequencing by hybridization (SBH), which uses interaction to dramatically reduce the number of oligonucleotides for de novo sequencing of large DNA fragments, while preserving the parallelism which is the primary advantage of SBH. The goals of the project include: (1) Development of efficient algorithms for the interactive design of sequencing chips; and (2) Utilization of simulation results to establish that 64kb fragments can be sequenced (obtained using approximately ten rounds of standard-sized 64k oligonucleotide arrays). The project includes the following theoretical and laboratory research in interactive SBH: (a) In a collaborative effort with biochemists at Oxford University, England, algorithmic issues in the design and manufacture SBH arrays, under a variety of fabrication technologies, are examined; (b) Algorithmic issues inherent in reconstructing DNA sequences from hybridization data, under complications such as non-classical chip designs and hybridization errors, are studied; and (c) Algorithmic issues inherent in other novel variations of SBH, particularly photolithography-based interactive SBH and positional SBH, are investigated. This project is jointly funded with the Computational Biological Activity.***