PromFD 1.0 – Predict Promoter Regions in DNA Sequences

PromFD 1.0

:: DESCRIPTION

PromFD is a computer program to recognize vertebrate RNA polymerase II promoters

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PromFD

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Feb;13(1):29-35.
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices.
Chen QK, Hertz GZ, Stormo GD.

EvoPromoter 0.9 – Finding Promoter Regions in Aligned Nucleotide sequences

EvoPromoter 0.9

:: DESCRIPTION

EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.

::DEVELOPER

EvoPromoter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • Java

:: DOWNLOAD

 EvoPromoter

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Aug 15;23(16):2031-7. Epub 2007 Jun 5.
Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.
Wong WS1, Nielsen R.

mmeta 1.0 – Align the TF-maps of Multiple Promoter Regions

mmeta 1.0

:: DESCRIPTION

mmeta is a program to produce and to align the TF-maps of multiple promoter regions. mmeta is very powerful to characterize promoter regions from multiple orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites.

::DEVELOPER

mmeta Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 mmeta

:: MORE INFORMATION

Citation

E. Blanco,R. Guigó and X. Messeguer
Multiple Non-Collinear Transcription Factor Map Alignment of Promoter Regions
BMC Bioinformatics 8:138 (2007).