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NestedMICA

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.

References:

To use NestedMICA, load the NestedMICA environment module.

module load NestedMICA

Environment variables set:

Interactive use

module load NestedMICA
cp $NMICA_DIR/micatest100.fa .
nminfer -seqs micatest100.fa -numMotifs 2 -minLength 4 -maxLength 12 -ensembleSize 50

sbatch

Create a batch input file (e.g. NestedMICA.sh). For example:

#!/bin/bash
module load NestedMICA
nminfer -seqs micatest100.fa -numMotifs 2 -minLength 4 -maxLength 12 -ensembleSize 50

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=1 NestedMICA.sh

Documentation