Welcome to BaMMServer

• What is the BaMM webserver?
  • Optimal input data
  • Understanding BaMMs
• Available workflows
  • De-novo motif discovery
    • Usage
      • General settings
      • Seeding stage
      • Refinement stage
      • Settings for further analyses
  • Motif scan
  • Motif database
  • Motif-motif comparison
• Understanding the output
  • Motif overview
  • Sequence logos
  • AvRec evaluation
    • Why yet another evaluation metric?
    • The method
    • Dataset AvRec vs. motif AvRec
    • The performance plots
      • P-value distribution plots
      • Recall vs. TP/FP ratio plots
  • Motif distribution plot
  • Motif-motif comparison
• File formats
  • Fasta
  • BaMM
  • MEME
  • Motif occurrence
  • Motif evaluation
• FAQ
  • How do I prepare my ChIP-seq data?
  • Can I use the server with long sequences (>250bp)?
  • Can I use the server with very few sequences?
  • How do I figure out whether my motif is biologically relevant?
    • Infer relevance from P-value distribution
    • Infer relevance from motif occurrences
    • Infer relevance from motif complexity
    • Infer relevance from MMcompare annotation
  • Where is the button to visualize in the genome browser?
• Miscellaneous
  • Glossary
  • Using the commandline tools
  • Setting up the server locally
• Citing BaMM webserver
• References