RIA: Optimization of DNA Sequencing Chips and Additional Biochemical Experiments for Sequencing by Hybridization

杂交测序（SBH）是一种具有挑战性的替代经典DNA测序方法。 对SBH的兴趣显著增长，已经导致构建了第一个测序芯片，通过SBH阅读前100 bp，并开发了用于构建高容量测序芯片的测序技术。 一些未解决的计算机科学问题严重减缓了SBH的生物化学和仪器方面的发展。 通过与生物学和SBH仪器组的密切合作，本项目确定并解决了以下计算机科学问题：（a）通过优化芯片进行序列重建的算法，（B）为SBH最佳选择附加生化实验的算法，（c）消除"盲“的算法。 通过SBH数据选择PCR引物，减少PCR反应的量， 分子进化研究中的常规测序，以及（d）结合联合收割机小规模SBH和引物步移的算法 DNA测序和并行化有序测序策略。

Sequencing by Hybridization (SBH) is a challenging alternative to the classical DNA sequencing methods. Remarkable growth of interest in SBH has already led to building the first sequencing chip, reading the first 100 bp by SBH and developing a photolithographic technique for building high-capacity sequencing chips. Some unsolved computer science problems seriously slow down the development of biochemical and instrumentation aspects of SBH. In close collaboration with biology and instrumentation SBH groups, the following computer science problems have been identified and are addressed by this project: (a) algorithms for sequence reconstruction by optimized chips, (b) algorithms to optimally choose additional biochemical experiments for SBH, (c) algorithms to eliminate ``blind'' choice of PCR primers by SBH data and reduce the amount of conventional sequencing in molecular evolution studies, and (d) algorithms to combine small-scale SBH and primer walking DNA sequencing and to parallelize ordered sequencing strategies.