Software Support for High-Throughput Sequence Reconstruction*

Charles Lawrence, Victor Solovyev, Ellen Bergeman, and Pam Culpepper.

Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030.

The Genome Reconstruction Manager (GRM) is an advanced software component for managing the data flow for high-throughput sequencing. A new release is currently available that includes the following features:

• Automation of preprocessing and assembly data flow.
• Computation of position-specific error probabilities for ABI sequence data.
• Use of position-specific error probabilities to support semi-automated editing of contigs.
• Use of position-specific error probabilities to support probability-based consensus computation and reporting of consensus sequence with confidence values.
• Computation of 'super contig' structure from pairwise distance and orientation constraints.
• Sequence assembly using the FAK 3.0 assembly kernel developed by E. Myeres and coworkers.
• Client-server based assembly (assembly may be performed on networked Sun or DEC Alpha hosts).
• Flexible visualization and interactive editing of contig multialignments and consensus sequence with coordinated display of aligned fluorescent traces.
• Seamless integration of all steps in a single application.

GRM runs on Sun workstations running Solaris 2.3 or 2.4.

For more information look at URL http://gc.bcm.tmc.edu:8088/GRM/grm-home.html or contact C. Lawrence (chas@bcm.tmc.edu).

*Supported by a grant from the DOE Human Genome Program, DE-FG-94ER61818

Lawrence, C.B, Honda, S., Parrott, N.W., Flood, T.C., Gu, L., Zhang, L., Jain, M., Larson, S., and Myers, E.W. 1994. The Genome Reconstruction Manager: A software environment for supporting high-throughput DNA sequencing. Genomics 23: 192-201.

Lawrence, C.B. and Solovyev, V.V. 1994. Assigning position-specific error probabilities to primary DNA sequence data. Nucl. Acids Res. 22: 1272-1280.