Services and Downloads

Web Services

Directed graphs over mixed data  types  
ComiR_logo_small Combinatorial microRNA target prediction  
miRconnX_logo Condition-specific mRNA-microRNA regulatory networks
stamp_logo_small Alignment, Similarity, & Database Matching for DNA Motifs
ASTRO_sm Analysis of Short Time-series using Rank Order preservation
enologos03asm energy normalized LOGOs
enologosC2H2a.smjpg energy normalized LOGOs of the C2H2 protein family
footersm finding mammalian transcription factor binding sites using phylogentic footprinting

Data Downloads

  • Manatakis, Raghu, Benos (2018) Bioinformatics (Proc ECCB 2018), 34:i848–i856 (pdf)
    • Simulated network data
    • Running example (for testing the code)
  • 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_logo_small STAMP version 1.1 (March 2008) ZIP archive
ssNPA version 1.0 (Dec 2019) Directory
MGM-FCI-MAX version 1.0 (May 2019) ZIP archive
piMGM version 1.0 (October 2018) ZIP archive
  HHMMiR version v1.2 (April 2009) ZIP archive