Cuticchia A J, Arnold J, Timberlake W E
Johns Hopkins School of Medicine, Baltimore, MD 21205.
Comput Appl Biosci. 1993 Apr;9(2):215-9. doi: 10.1093/bioinformatics/9.2.215.
In the program ODS we provide a methodology for quickly ordering random clones into a physical map. The process of ordering individual clones with respect to their position along a chromosome is based on the similarity of binary signatures assigned to each clone. This binary signature is obtained by hybridizing each clone to a panel of oligonucleotide probes. By using the fact that the amount of overlap between any two clones is reflected in the similarity of their binary signatures, it is possible to reconstruct a chromosome by minimizing the sum of linking distances between an ordered sequence of clones. Unlike other programs for physical mapping, ODS is very general in the types of data that can be utilized for chromosome reconstruction. Any trait that can be scored in a presence--absence manner, such as hybridized synthetic oligonucleotides, restriction endonuclease recognition sites or single copy landmarks, can be used for analysis. Furthermore, the computational requirements for the construction of large physical maps can be measured in a matter of hours on work-stations such as the VAX2000.
在ODS程序中，我们提供了一种将随机克隆快速排列到物理图谱中的方法。根据分配给每个克隆的二进制签名的相似性，将单个克隆按照其在染色体上的位置进行排序。该二进制签名是通过将每个克隆与一组寡核苷酸探针杂交获得的。利用任意两个克隆之间的重叠量反映在它们二进制签名的相似性这一事实，可以通过最小化有序克隆序列之间的连接距离之和来重建染色体。与其他物理图谱构建程序不同，ODS在可用于染色体重建的数据类型方面非常通用。任何可以以存在或不存在的方式进行评分的特征，如杂交的合成寡核苷酸、限制性内切酶识别位点或单拷贝标记，都可用于分析。此外，在VAX2000等工作站上，构建大型物理图谱的计算需求在数小时内即可完成。
