-->

Services
	Condition-specific mRNA-microRNA regulatory networks
	(Looking for mirConnect? Click here)
	Analysis of Short Time-series using Rank Order preservation
	energy normalized LOGOs
	energy normalized LOGOs of the C2H2 protein family
	finding mammalian transcription factor binding sites using phylogentic footprinting
	Alignment, Similarity, & Database Matching for DNA Motifs
TRANSFAC ®	BIOBASE database and tools (internal access only - pswd required)
Data Downloads
Corcoran, Pandit et al. (2009) PLoS ONE, 4:e5279 (pdf) raw ChIP-chip data training datasets Kadri et al. (2009) APBC/BMC Bioinformatics, 10(Suppl 1):S35 (pdf) miRNA cross-species characteristics HHMMiR algorithm Training and testing datasets Mahony et al. (2007) Genome Biol 8: R84 (pdf) README file (text - description fo the dataset files) Datasets (protein coding, microRNA, tRNA and developmental gene datasets) Mahony et al. (2007) ISMB (Proc ISMB) 23: i297-i304 (pdf) README file (text - description fo the dataset files) Dataset (ZIP archive file) Mahony et al. (2007) PLoS Comput Biol 3: e61 (pdf) Supplementary Table (performance of strategies for aligning DNA motifs - complete list) PSSM models with the corresponding family of each transcription factor Mahony et al. (2006) Neural Networks 19: 950-962 (pdf) Supplementary Table (Comparing motif-finders in 77 yeast datasets) Corcoran et al. (2005) Nucl Acids Res 33(Web Server issue): W442-W446 (pdf) Supplementary Table (Footer predictions) Corcoran et al. (2005) Genome Res 15: 840-847 (pdf) Supplementary Table 1 (Footer predictions) Supplementary Table 2 (comparison with other methods) Promoter regions (test set) DBA alignments PSSM models Benos et al. (2002) J Mol Biol 323: 701-727 (pdf) EGR selection dataset (SAMIE training set) SAMIE EGR model
Software Downloads
	STAMP version 1.1 (March 2008) ZIP archive
	HHMMiR version v1.2 (April 2009) ZIP archive

• 
• 
• 
• 
• 
• 
• 
  • 
  • 
  • 
  • 
  • 
  • 
  • 
  • 
• 
  • 
  • 
•