Livermore’s Pragmatic Approach to Integrated Mapping for Chromosome 19

Abstract

For several years Livermore has been using a bottom-up approach to physical mapping, constructing contigs from cosmid clone fingerprints. We currently have 7112 clones placed in 854 contigs and now are using various other means to close gaps, complete, and verify the map. This has required us to develop an information model capable of handling all the important relationships between any “mappable object” and producing a variety of ways of visualizing this integrated data. We have defined a set of relations on a single generic map object class that allows us to distill all the distance/order/orientation/overlap/etc. data contained in our underlying database, along with algorithms to construct partial order trees and display the integrated results in our X-windows database browser tool. This system uses Sybase/SQL/Unix/C and can be used on Sun color Sparcstations with Internet access. We currently have SQL access to the GDB and GenBank database servers but are not yet extracting relevant data from these sources into our integrated map except through our direct collaborations with data submitters. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. W7405-ENG-48.