Advanced Pattern Search Toolkit for Sequential Data

Overview

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Platform requirements

Operating systems:

• With APaS and BioPAT for Java™: Any Java platform
• With BioPAT for C++:
  • Linux® platform with Red Hat distribution, Version 9.0
  • Pentium® or above processors
  • GCC Version 3.2.2-5

Software:

• JRE 1.4.2 or above
• JDK 1.2 or above for application development

Installation instructions

If using APaS Toolkit for Sequential Data:

1. Unzip the file APaS.zip into a directory. Within are six JAR files:
   • APST.jar contains the tools and the core engine.
   • Ugene.jar contains the code and classes for a sample GUI application for demonstrating the gene-finding tool.
   • Samples.jar contains the code and classes for a sample command line application that demonstrates the gene-finding and generic pattern-finding tools.
   • APaS 1.0 uses MetaStuff's dom4j library for processing XML documents. dom4j is distributed along with APaS 1.0 in dom4j-core.jar. Further information is available at http://dom4j.org/.
   • APaS 1.0 uses Apaches Xerces2 Java Parser for processing XML documents. Xerces2 is distributed along with APaS 1.0 in xerces.jar. Further information is available at http://dom4j.org/.
   • APaS 1.0 uses Regex for Java, a Java-based pattern recognition tool. Regex for Java is districbuted along with APaS 1.0 in regex4j.jar. Further information is available here on alphaWorks.
2. Include the following four JAR files in your classpath:
   • APST.jar
   • dom4j-core.jar
   • xerces.jar
   • regex4j.jar
3. Client code may be built around the classes made available. Please refer to the Javadocs for API details.

   The stand-alone applications that demonstrate the engine may be run from command prompt as follows:

   • Run Ugene.bat for the GUI version of the Gene-Finding tool (you can use GeneInput.xml as test input).
   • Run GeneFinder.bat for the command line version of the Gene-Finding tool (you can use GeneInput.xml as test input).
   • Run PatternFinder.bat for the command line version of the Generic Pattern-Mining tool (you can use TextSearch.xml as test input).

If using BioPAT for Java and C++:

1. The BioPAT for Java utility class library is contained in biopat4j.zip. Detailed instructions for use are provided in Section 3 of the The Advanced Pattern Search Toolkit for Sequence Data whitepaper.doc, included in the current release. The API documentation is in the directory BIOPAT4J_api within the biopat4j.zip package.
2. The BioPAT for C++ utility class library is contained in Biopat-0.9.zip. Detailed instructions for use are provided in Section 4 of the The Advanced Pattern Search Toolkit for Sequence Data whitepaper.doc, included in the current release. The API documentation is in the zip file Docs.zip within the Biopat-0.9.zip package.

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