Abstracts: 

 Informatics 



Human Genome Center, Lawrence Berkeley Laboratory 



Charles R. Cantor, W. Chang. D. Gusfield, M. Hutchinson. W. Johnston. G. Lavvler. 

 P. Li. V. Markowitz. D. Naor. F. Olken. and C. L. Smith 

 Human Genome Center. Lawrence Berkeley Laboratory. Berkeley. CA 94720 

 (415) 486-6800. ( FTS ) 4.S 1 -6800 



Researchers at the Human Genome Center at Lawrence Berkeley Laboratory (LBL) are 

 developing computational tools needed to analyze the map. clone, and sequence data 

 generated from human genome research and to provide the technical foundation for the 

 construction of a Human Genome Information System (HGIS). Plans call for the 

 development of logical data models, physical structures, access methods, and query 

 facilities for map and sequence data. Also to be investigated are methods for fragment 

 overlap detection, map assembly, and approximate sequence and pattern matching. 



Brief abstracts of the individual projects are listed below. 



Chromosome-21 Database (W. Johnston. F. Olken. and C. L. Smith) — The current 

 goal in database management for maps and sequences is a prototype, integrated 

 chromosome-21 database and mapping system. The system is initially targeted at 

 groups involved in developing the physical map of chromosome 21 but can be extended 

 to groups studying other aspects of chromosome 21. This system will provide access to 

 various types of physical, cytogenetic, and genetic maps of chromosome 21; a 

 bibliography of chromosome-2 1 literature; map construction algorithms; and graphic 

 tools for drawing, displaying, and editing maps. 



Computer-Assisted Laboratory Notebook (W. Johnston. M. Hutchinson, 

 V. Markowitz, F. Olken. and C. L. Smith) — Image storage and indexing for gen- 

 erating physical maps requires interfacing a data management system with a mass 

 storage facility. The data management group has made progress in using an extended 

 entity relationship as a basis for a data management system that will combine elements 

 of a graphical and textual interface with data interchange between numerous 

 repositories of data. This system will allow data to be loaded in such a way that the data 

 can be updated, edited, reviewed, queried, and manipulated with ease. The computer- 

 assisted laboratory notebook also provides a means of tracking individual experiments, 

 handling inventories, and integrating data for the development of physical maps. 



Theory Group (W. Chang. D. Gusfield. G. Lawler. P. Li. and D. Naor) —Theoretical 

 work IS being done on two problems: string matching for sequence alignment and map 

 assembly for probed partial digestion experiments. The map assembly effort has looked 

 at backtracking algorithms, including various special cases (e.g.. probes on adjacent 

 fragments). In the coming year these researchers expect to continue their investigations 

 and look especially at incorporating polymorphism data and multiprobe experiments. 

 The string-matching work has yielded a fast algorithm for approximate string matching 

 with a bounded number of errors. Also expected to be improved are the error-handling 

 abilities of the algorithm. 



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