Using Comparative Genomics for Whole Genome Discovery of Regulatory Elements in Vertebrates
Amol Prakash, Martin Tompa


All data is obtained from Ensembl (version 26)
Datasets having high confidence homologous promoter sequences
1. Human/Chimp/Mouse/Rat
2. Human/Chimp/Mouse/Rat/Chicken
3. Human/Chimp/Mouse/Rat/Chicken/Fugu


Clustering results (Listing only Clusters of size at least 2)
1. Stringent Clustering on Human/Chimp/Mouse/Rat       Motif Clusters       Cluster Size Distribution
2. Permissive Clustering on Human/Chimp/Mouse/Rat       Motif Clusters       Cluster Size Distribution
3. Stringent Clustering on Human/Chimp/Mouse/Rat/Chicken       Motif Clusters       Cluster Size Distribution
4. Stringent Clustering on Human/Chimp/Mouse/Rat/Chicken/Fugu       Motif Clusters       Cluster Size Distribution

Phylogenetic tree relating the species used in the analysis: Relevant parameters for the various tools used in the study
Footprinter : -size 10 -max_mutations 2 -max_mutations_per_branch 2 -sequence_type upstream
MLAGAN : default parameters
ClustalW : -endgaps
MAVID : No parameters to tune
DIALIGN (version2) : default parameters
TBA (BlastZ) : T=0 W=3 B=0 C=2 K=500

For more details, write to : tompa[AT]cs.washington.edu