Research Facility 

 Narratives: LBL 



Restriction map of the entire S. pombe genome completed. 



Second-generation mapping strategy designed — to be implemented using the 

 polymerase chain reaction (PCR) and automated-sequencing procedures. LBL's 

 strategy is to use DNA sequences troni the ends of the fragments as unique "I. D." tags. 

 Matching these DNA sequences with similarly sized DNA sequences from linking 

 clones (clones that contain DNA from the ends of adjacent large fragments) will 

 facilitate map construction. The advantages of this protocol over others is the speed 

 with which results are generated, the precision of ordering, the simplicity of data 

 analysis, and the fact that the mapping process generates sequence data as well. 



Computer-controlled pulsed-field gel (PF(;) electrophoresis apparatus constructed 

 and used to discover new pulse shapes that speed separations five- to tenfold. The 



test apparatus consists of a 24-node computer-controlled power supply that is capable of 

 independently programming the pulse sequence of individual electrodes. Computer 

 calculations are used to define the electrode voltage distribution required to generate 

 specific electric field profiles within the gel. During the run, a three-dimensional 

 precision manipulator allows computer-controlled scanning of the gel to monitor 

 parameters such as voltage, ionic strength. pH. and temperature. 



Interactive computer processing of gel images developed so that collection of over- 

 and underexposed areas eliminates the need for repeating exposure times. This 

 program provides fully automatic analysis of the separated DNA, if desired; however, 

 the operator has the option to substitute his/her own judgement at every step. The data 

 sets of separated DNA are subsequently used for algorithmic comparisons between 

 lanes and gels, as well as in mapping algorithms, and are stored in a laboratory 

 database. 



New computational algorithms for map assembly developed. Dynamic programming 

 algorithm.s — traditionally, the technique of choice for matching problems — are likely to 

 be impracticable for problems of the size generated by human genomic research. For 

 this purpose. LBL has worked to extend the use of suffix trees: the objective is to 

 develop computational methods that are faster and more practical than current ones. 



New model for map assembly data management systems (based on extended- 

 entity-relationship model) designed. LBL researchers are using a database schema 

 design tool (SDT) developed at LBL to provide a powert'ul and easy-to-use interface for 

 biologists and to increase the productivity of the database design process. 



Mapping the telomere of human chromosome 4, which contains the gene for 

 Huntington's disease, initiated. Probes have been developed to recognize a telomeric 



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