EMMA 1.1 – Prediction & Alignment of Cis-regulatory Modules

EMMA 1.1

:: DESCRIPTION

EMMA (Evolutionary Model-based cis-regulatory Module Analysis) is meant for prediction of regulatory targets of a motif using two-species comparison. If you have a sequence window of length ~100 bp – 2000 bp, and its orthologous window from another species, use EMMA to score the window for matches to a given motif. EMMA is also useful for alignment of cis-regulatory modules (enhancers) between two species, if you have knowledge of the relevant transcription factor motifs.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

EMMA

:: MORE INFORMATION

Citation

LoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299.
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
He X, Ling X, Sinha S.

EMMA 1.1.2 – Efficient Mixed-Model Association

EMMA 1.1.2

:: DESCRIPTION

EMMA (Efficient Mixed-Model Association) is a statistical test for model organisms association mapping correcting for the confounding from population structure and genetic relatedness. EMMA takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to sustantially increase the computational speed and the reliability of the results.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 EMMA

:: MORE INFORMATION

Citation

Hyun Min Kang , Noah A. Zaitlen , Claire M. Wade, Andrew Kirby , David Heckerman, Mark J. Daly and Eleazar Eskin
Efficient Control of Population Structure in Model Organism Association Mapping.
Genetics. 2008 Mar;178(3):1709-23.