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