Supplementary material for

"CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting" Bigelow et al. (2004, BMC Bioinformatics).

• Supplementary figure
• go to the CisOrtho website
• Download Manuals and Instructions for Web based CisOrtho
• download CisOrtho:
  from here you may download the entire software suite and associated input files. The README file gives detailed instructions.
  cisortho.tgz (c++ source code and program input files as a linux archive)
  cisortho.zip (c++ source code and program input files as a mac or win archive)
  

  (Note: The distribution is easily compiled for Linux. I haven't yet succeeded in porting this to Windows or Mac. Please contact me (Henry Bigelow, hrb46@columbia.edu) if you either succeed in doing this or would like me to do it.

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  Required Additional Software

  opt-3.19.tar.gz
  hmmer-2.3.2.tar.gz
  

General protocols (from Ambros lab page)

>> click here

PCR protocol for rapid generation of PCR fusions

>> click here

Efficient protocol for integration of extrachromosomal arrays

>> click here