NestedMICA is a method for discovering over-represented short motifs in large sets of strings. Typical applications include finding candidate transcription factor binding sites in DNA sequences.
How to Use
You will need to set your environment using the commandmodule load NestedMICA
To find all versions of NestedMICA, typemodule avail NestedMICA
Then you simply call the commands. Here is a simple example. After first loading the NestedMICA module, type:cp $NMICA_DIR/micatest100.fa . nminfer -seqs micatest100.fa -numMotifs 2 -minLength 4 -maxLength 12 -ensembleSize 50