BaMMserver
What is the BaMM webserver?
Available workflows
Understanding the output
File formats
FAQ
Miscellaneous
Citing BaMM webserver
References
BaMMserver
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Welcome to BaMMServer
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Welcome to BaMMServer
ΒΆ
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
Read the Docs
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