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

Here is a sample qsub script nmica.sh:

#!/bin/bash
#PBS -N nmica
#PBS -e nmica.err
#PBS -o nmica.out
cd $PBS_O_WORKDIR
module load NestedMICA
nminfer -seqs micatest100.fa -numMotifs 2 -minLength 4 -maxLength 12 -ensembleSize 50

Submit this to the cluster using the command:

qsub -l nodes=1 nmica.sh

Documentation

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