Custom Developed Software

Plasmodium falciparum high-density microarray analysis software. Dharia et al (2009) Use of high-density tiling microarrays to globally identify mutations and elucidate mechanisms of drug resistance in Plasmodium falciparum. Genome Biology, 10:R21. [PubMed]

  • Visualize microarray data.
  • Detect copy number variations (CNVs) rapidly and accurately.
  • Identify and visualize predicted single nucleotide polymorphisms (SNPs) in the genome.
  • All performed in a single overnight hybridization followed by quick computational analysis.

About: Our software package is available with the complete source code for download. As this is the first release, we expect there are bugs and errors that may occur. To help us further improve the software, please email Neekesh Dharia at ndharia@scripps.edu with any problems or comments.

Microarray Data: Download CEL files for Dharia et al Genome Biology 2009, 10:R21.

Software Versions:
MATLAB-dependent version 1.0
  • System Requirements: MATLAB 7.5 or newer with statistics toolbox required. 4 GB RAM recommended. Compatible with Mac OS X and Windows. There are text formatting issues that have not been resolved when using the software in Windows.
  • Download PftilingAnalysis_v1_0.zip (146.6 MB)
Standalone version 1.0 (Mac OS X)
  • System Requirements: Mac OS X 10.4 (10.4.8 and above) or Mac OS X 10.5 (10.5.1 and above). Intel processors. 4 GB RAM recommended. PPC is no longer supported by MATLAB and thus is not supported by our application.
  • Download PftilingAnalysis_v1_0_maci_pkg (349.8 MB)
  • Problems with uneditable text boxes? If you have "Java for Mac OS X 10.5 Update 2" installed this is a known problem, here is a fix: Download and unzip the following version of Java 1.5.0: Java1p5.tar.gz (93.5 MB). Delete the 1.5.0 folder from /System/Library/Frameworks/JavaVM.framework/Versions/ and replace it with the newly downloaded version.
Standalone version 1.0 (Windows)
  • System Requirements: Windows XP (Service Pack 1, 2 or 3), Windows Server 2003 (Service Pack 1 or 2, R2) or Windows Vista (Service Pack 1). 4 GB RAM recommended. Intel Pentium (Pentium 4 and above), Intel Celeron, Intel Xeon, Intel Core, AMD Athlon 64, AMD Opteron, or AMD Sempron processors. 4 GB RAM recommended. There are text formatting issues that have not been resolved with the Windows version of the software.
  • Download PftilingAnalysis_v1_0_win_pkg.exe (315.4 MB)

Databases: All gene and chromosome information and annotation was from PlasmoDB version 5.3. We expect a new release in the next few months updated to reflect the newest version of PlasmoDB (currently 5.5).