Development of Protocols for the Beckman CEQ 2000 sequencer

    We have been using the CEQ sequencer for de novo genome sequencing, polymorphism discovery, quality control of microarray clone sets, and fragment analysis.  A number of our improvements to the hardware, software and protocols have been incorporated by Beckman Coulter.  Some of our results are reported in:

Kari A. Kukanskis, Zakir Siddiquee, Ralph V. Shohet, H. R. Garner, " A mix of sequencing technologies for sequence closure: An example," BioTechniques, 1999.

    UTSW and Beckman-Coulter are collaborating on developing protocols, instrumentation and software for the enhancement and demonstration of the CEQ 2000 capillary sequencer.

    We have recently completed version 1 of our code SNPCEQer, a code written to take advantage of the quality values generated uniquely by the Beckman CEQ 2000 and 8000 sequencers.  This code is available for download, but is not supported by our group.  This code takes a collection of sequence read files, performs a multiple alignment and then calls and outputs the high quality discrepancies as putative SNPs.  Newer versions with integrated chromatogram viewing are planned.  Please download the code from our SNPCEQer page.

• Project Goals
• CEQ Specifications
• Experiments
• Protocols

    For further information contact Elizabeth Flood in our group or Beckman Coulter Instruments, www.beckman.com