Software Designed for Motif and motif module discovery in high-throughput sequencing data sets

SIOMICS Software Download

Software Version Manual Changelog
SIOMICS 3.0 (For Windows)
SIOMICS 3.0 (For Linux)
(Mar 22,2016)
SIOMICS 3.0 Major updates:
(1) Enabled Monad, Dyad, Monad+Dyad motif prediction modes.
(2) Enabled default/iterative modes. Iterative mode can be used to identify statistically insignificant motifs, but it's much more time consuming.
(3) Enabled User-defined motif database comparsion. Users can specifiy known motif databse, which the predicted motifs will be compared to.
(4) Added STAMP E-value cutoff parameter, users can choose specific E-value cutoff for motif comparsion (between the predicted motifs and known motifs in database)
(5) Enabled length-variable motif prediction. Users do not need to specify the length for predicted motifs (like DREME, peaks-motifs).
(6) Motif redundancy was reduced significantly.
SIOMICS 2.0 (For Windows)
SIOMICS 2.0 (For Linux)
(Mar 20,2014)
SIOMICS 2.0 Major updates:
(1) The length of predicted motifs can be automatically adjusted.
(2) Added 3 more options -e -t -y to the software to indicate whether the extension, comparison or visualization will be performed.
(3) Added More details about extension results. (7 results files for extension were provided).
SIOMICS 1.4 (For Windows)
SIOMICS 1.4 (For Linux)
(Nov 22,2013)
SIOMICS 1.4 Minor updates:
(1) Make SIOMICS compatible for Java 6 and Java 7.
(2) Changed the multiple comparison correction.
(3) Add X.motifs.tfbs.inModule as one of the predictions.
SIOMICS 1.2 (For Windows)
SIOMICS 1.2 (For Linux)
(Jul 16,2013)
SIOMICS 1.2 The initial distribution version of SIOMICS

Note: Please use the most updated SIOMICS version for more enabled features. If you have encountered any bugs, please report to or