Automated DNA sequence data management and analysis with the Finch™-Chromatogram Server
     Todd M. Smith, Joe Slagel, Chris Abajian, Dave Campbell
     Geospiza, Inc., Seattle, WA

 DNA sequencing is a multistep process in which large numbers of small template clones are propagated, purified, sequenced and analyzed on acrylamide gels. A challenge to low-cost high-throughput DNA sequencing is a lack of robust software tools that support automated data entry, storage, retrieval, and analysis. Further challenges to core sequencing facilities include registering and tracking samples provided by clients. Commercial tools are needed that provide methods for recording and combining laboratory workflow information with data quality analysis.

Geospiza's Finch™-Chromatogram Server provides a low cost turn-key solution for storing, managing and archiving chromatogram files from PE-ABD 373 and 377 DNA sequencers. A web-based interface allows for platform independent access and operation. Data quality is checked with the phred base calling algorithm (Ewing, B. et. al. Genome Research, 1998). The resulting sequences are automatically checked for vector, E. coli and other sequence-based artifacts using cross_match (Green, P., unpublished). Quality and analysis information are stored in an embedded relational database management system that provides secure access to data for multiple users. Additional features include quality assurance reports and an simple interface that allows for user-initiated queries.

The chromatogram server is scalable, operates on a variety of UNIX-based computer platforms, including Pentium PCs running Linux, and is well suited for production centers, core facilities and research laboratories. A complete solution for data collection and analysis is achieved when the chromatogram server is combined with other components in the FinchTM-Suite.

 Association of Biomolecular Resource Facilities Conference, 1999