The Gene Discovery workbench, for which a prototype was realized during Phase I, seeks to enable researchers working on genomic sequencing projects to make extensive and efficient use of the available computational tools for interpreting data from DNA sequencing experiments. The GDW software package will will provide an intuitive user environment for Windows and Mac systems that joins a wide number of sequence analysis methods under one common interface while automating access to databases and analysis engines available on the Internet or corporate intranet. This package will have a modular architecture that permits users to add or remove analytical methods from the program. Modules will include gene-finding algorithms such as Genemark or GenScan, similarity search methods such as BLAST or Prosite, and common sequence analysis techniques such as dot-plots, alignment editors and charge plot calculators. The combination of a number of methods is highly successful in accurate gene identification by tempering the weakness of one technique with the strengths of another. While it is now necessary to install a number of packages on several operating systems and spend tedious hours converting between different file formats and computer platforms to get accurate and comprehensive data for gene-identification, the GDW will join all the methods under one common interface and handle network queries, format translations, and parsing results into readable results and graphical representations ready for publication. The package will also provide a robust environment for annotating biological. No other package today provides this level of ease or functionality, despite it~s obvious immense benefits in accelerating the interpretation of data from industrial, academic, and medical genetic research.
