SBIR-STTR Award

We intend to develop a multimedia computer system that will be able (i) to manage the DNA and protein sequence data generated by a gene discovery project, (ii) to help the user to choose the most appropriate method for a given task and (iii) to combine several methods for solving an overall problem. Recently a combination of extrinsic, BLAST type, and intrinsic, GeneMark, methods was shown to be successful in accurate gene identification. It was also shown that genes that were not detected by a similarity search could be identified by a combination of several gene statistical models . We will create an interactive environment for simultaneous application of several DNA and protein sequence analysis methods by merging local programs employing the methods of intrinsic statistical analysis with extrinsic (external) procedures that require Internet and World Wide Web telecommunication. The system will be developed for IBM PC and MAC platforms using the latest network protocols. Such a computer workbench for a gene discovery will be affordable for the vast majority of the potential users.Proposed commercial application:The new computer technology for efficient handling of sequence data, generated by gene discovery projects will be made available for the academic/industrial community. This technology should speed up expensive genomic sequencing experiments i) by helping to interpret DNA and protein sequence features; ii) by focusing into sequence problematic domain, iii) by facilitating rational primers design for RT-PCR experiments; iv) by providing information for efficient screening of cDNA libraries.National Center for Human Genome Research (NCHGR)

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.Thesaurus termscomputer assisted sequence analysis, computer human interaction, computer program /software, computer system design /evaluation, interactive multimedia, method development, nucleic acid sequence Internet, computer network, genome, protein sequenceNational Institute of Human Genome (NIHG)