Description

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 command

module load NestedMICA

To find all versions of NestedMICA, type

module avail NestedMICA

Please see here for more information about environment modules.

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

Documentation

• NestedMICA as an ab initio protein motif discovery tool (2008, PubMed)
• NestedMICA Home
• The NestedMICA motif inference tool (PDF)