ELPH : Estimated Locations of Pattern Hits

Overview

ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). See below for instructions on downloading the complete system, including source code. 
An online tool that uses ELPH output for identifying exon splicing enhancers can be found here.

System requirements

ELPH is released as source code and was tested on Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1, but should work on any Unix system.

Obtaining ELPH

This software is  OSI Certified Open Source Software .

To download the complete ELPH system, just click here .

% tar -xzf ELPH.tar.gz

A directory named 'ELPH/' will be created which contains the executable, training data sets, and other supporting files.

Documentation

A basic user manual for ELPH is available here.

Contact Information

Use this form to contact us.

Acknowledgements

The project is supported in part by NSF Award MCB-0114792, "Arabidopsis 2010: Pre-mRNA Splicing Signals in Arabidopsis".

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