Management of evolving map data: data structures and algorithms based on the framework map.
A consensus framework map of a chromosome is the single most useful map of the chromosome, because of the amount of information it holds as well as the quality of the supporting data backing the putative order of its objects. We describe data structures and algorithms to assist in framework map maintenance and to answer queries about order and distance on genomic objects. We show how these algorithms are efficiently implemented in a client-server relational database. We believe that our data structures are particularly suitable for databases to support collaborative mapping efforts that use heterogeneous methodologies. We summarize two applications that use these algorithms: CHROMINFO, a database specifically designed for framework map maintenance; and the shared client-server database for the chromosome 12 genome center.
Nadkarni
P M
PM
Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut 06510, USA. nadkarni@cs.yale.edu
D000465:Algorithms; D002874:Chromosome Mapping; D008792:Metric System