ODS: ordering DNA sequences—a physical mapping algorithm based on simulated annealing

• Published in: Bioinformatics 1993-04, Vol.9 (2), p.215-219
• Main Authors: Cuticchia, A.J., Arnold, J., Timberlake, W.E.
• Format: Article
• Language: English
• Subjects: Algorithms; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Chromosome Mapping; DNA Fingerprinting; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Models, Molecular; Nucleic Acid Hybridization; Nucleic acids; Sequence Analysis, DNA - methods; Software Design
• ISSN: 1367-4803; 0266-7061; 1460-2059
• 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 workstations such as the VAX2000.