The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis

Abstract

Summary: With PACRAT (Patterns, Analyses, Correlations. Remote Archive Testbed) we present an online database solution to the problem of accessing high-confidence sequences with specific relationships to classes of genes, such as upstream intergenic regions attached to tRNA genes. In addition the software contains a data warehousing and analysis-facilitating suite to streamline the process of analyzing the collected data. An unexpected additional benefit of the system is that it also provides easy access to sequences of lower confidence, and may be of assistance in such things as resolving ORF-call conflicts in genomic annotation projects. Availability: An instance of the PACRAT system, implemented on a set of archaeal genomes, an experimental version of a Yeast genome database, and a random sequence database, is available for use at http://www.biosci.ohio-state.edu/~pacrat/. The system is also available for download for installation of local project-oriented sites. See the online PACRAT ‘About’ page for details. Contact: ray@biosci.ohio-state.edu; daniels.7@osu.edu Supplemental information: Additional information regarding the PACRAT system, including sample datasets is available linked from the ‘About’ page of the PACRAT website at: http://www.biosci.ohio-state.edu/~pacrat/.