SMoD
SequenceMotifDecomposer (SMoD) is a motif finder algorithm based on the EDeN framework.
Installation
SMoD can be installed via conda:
conda install smod -c biocondaUsage
SMoD can be invoked as:
./smod --pos data.fa -t 1 --freq_th 0 --std_th 0Output
The program outputs a file called report.md in Markdown format.
One can then convert it to html or pdf with appropriate utilities (e.g. markdown2pdf )
Help
SequenceMotifDecomposer (SMoD) is a motif finder algorithm.
Version: 1.0
Author: Fabrizio Costa [costa@informatik.uni-freiburg.de]
Usage:
smod -i FILE (--neg FILE | -t N) [-m FILE] [-o PATH] [-n N] [-p N]
[-c N] [--min_subarray_size N] [--max_subarray_size N]
[--similarity_th N] [--min_score N] [--min_freq N]
[--min_cluster_size N] [--regex_th N] [--sample_size N]
[--freq_th N] [--std_th N]
[--verbose]
smod (-h | --help)
smod --version
Options:
-i FILE Specify input fasta file for positive seqs.
--neg FILE Specify input fasta file for negative seqs.
-m FILE Model file. If specified no fitting is performed
[default: None]
-t N The num of permutations for each positive
sequence [default: 1].
-c N Feature complexity [default: 5].
-p N P-value [default: 0.05].
-n N Specify the num of clusters [default: 20].
-o PATH Dir name for output files [default: out].
--min_subarray_size N The min num of nt in a motif [default: 4].
--max_subarray_size N The max num of nt in a motif [default: 10].
--similarity_th N The min relative edit distance to merge two motives
[default: 0.5].
--min_score N The min num of nt in a motif that need to have a
freq > min_freq [default: 4].
--min_freq N Min freq in the alignment [default: 0.5].
--min_cluster_size N Min num of seqs selected for a motif [default: 10].
--regex_th N Min freq for a nt to be selected in the regex
expression [default: 0.3].
--sample_size N The num of sequences randomly sampled to
build the alignment for a motif [default: 200].
--freq_th N The min freq of a regex seq (use 0 to deactivate)
[default: 0.03].
--std_th N The max standard deviation for the localization of a
rgex seq (use 0 to deactivate) [default: 25].
-h --help Show this screen.
--version Show version.
--verbose Print more text.