论文标题
新的字符串编辑距离和应用
A New String Edit Distance and Applications
论文作者
论文摘要
字符串编辑距离已经使用了数十年,从拼写校正和Web搜索建议到DNA分析等等。大多数字符串编辑距离是Levenshtein距离的变化,仅考虑单字符编辑。在法医应用中,使用了多态性遗传标记,例如短串联重复序列(STR)。在这些重复的基序中,DNA复制误差不仅包括单个基本差异。经常观察到``口吃''的现象,其中重复单元的数量(按整个单位)与模板不同。为了适应Levenshtein距离,适用于感兴趣的DNA序列相似性的法医应用,定义了一个广义的字符串编辑距离,该距离可容纳除单核苷酸编辑外的整个基序的添加或缺失。开发了用于计算序列之间的距离的动态编程实现。该算法的新颖性在于处理多个字符和单字符编辑之间出现的复杂相互作用。法医示例说明了限制的法医利文斯素(RFL)距离度量的目的和使用,但应用扩展到其他生物学区域中的序列比对和字符串相似性,以及动态编程算法更广泛。
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only single-character edits. In forensic applications polymorphic genetic markers such as short tandem repeats (STRs) are used. At these repetitive motifs the DNA copying errors consist of more than just single base differences. More often the phenomenon of ``stutter'' is observed, where the number of repeated units differs (by whole units) from the template. To adapt the Levenshtein distance to be suitable for forensic applications where DNA sequence similarity is of interest, a generalized string edit distance is defined that accommodates the addition or deletion of whole motifs in addition to single-nucleotide edits. A dynamic programming implementation is developed for computing this distance between sequences. The novelty of this algorithm is in handling the complex interactions that arise between multiple- and single-character edits. Forensic examples illustrate the purpose and use of the Restricted Forensic Levenshtein (RFL) distance measure, but applications extend to sequence alignment and string similarity in other biological areas, as well as dynamic programming algorithms more broadly.