Software Releases:The computational tools we have developed are available for download and free use by the academic community.

EMMA (Prediction and alignment of cis-regulatory modules)

This Linux-based program 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. 

GenomeSurveyor (Prediction of motif targets in D. melanogaster)

This web-based Genome Browser allows you to find regulatory targets of a large collection of transcription factors in the Drosophila genome. You may use cross-species comparison among 12 genomes to see conserved targets.

CRM discovery benchmark (Data sets from D. melanogaster.)

Morph software (Probabilistic alignment of cis-regulatory modules)

D2Z software (Alignment free comparison of regulatory sequences.)

Indelign software (Probabilistically annotating indels in multiple alignments)

DIPS software (For finding discriminative PWM motifs)

Stubb software   Stubb Web Server    (For finding cis-regulatory modules)

Stubb software Stubb Web Server (For finding cis-regulatory modules)

YMF software YMF Web Server (Motif finding)

PhyME software (Motif finding in orthologous sequences)