PANTHER provides a number of useful research tools, including the PANTHER HMM Scoring Tool, cSNP Analysis Tool, and Gene List Analysis Tool. Both the PANTHER HMM Scoring Tool and cSNP Analysis Tools have online and downloadable versions. The online versions allow only one protein sequence to be analyzed at a time, while the downloadable versions allow large batch analyses. A brief description of the downloadable version of PANTHER HMM Scoring Tool can be found in Box 2. The details of how to use these tools can be found in the PANTHER help page (http://www.pantherdb.org/help/PANTHERhelp.jsp) and the user manual. In this protocol, we will focus on the Gene List Analysis Tool. Sample gene list files can be found in the Supplement materials for testing.
