The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common type of synthesis process where multiple DNA strands are synthesized in parallel from a common alternating supersequence, one nucleotide at a time. The synthesis time or the number of synthesis cycles is then determined by the length of this common supersequence. In this model, we design quaternary codes that minimizes synthesis time that can correct deletions or insertions, which are the most prevalent types of error in array-based synthesis. We also propose polynomial-time algorithms that encode binary strings into these codes and show that the rate is close to capacity.

翻译：DNA链的合成仍是DNA存储系统中最昂贵的环节。因此，为使DNA存储系统更具实用性，需优化合成过程中使用的时间与材料。本文考虑了最常见的合成过程类型——多根DNA链通过共同交替超序列并行合成，每次仅合成一个核苷酸。此时，合成时间或合成周期数由该共同超序列的长度决定。在此模型下，我们设计了能最小化合成时间且可纠正删除或插入错误的四进制编码——这些错误是阵列合成中最常见的错误类型。我们还提出了将二进制字符串编码为这些编码的多项式时间算法，并表明其编码率接近容量上限。