SIOMICS3 is a software used to de novo identify monad/dyad motifs from TF-based ChIP-seq datasets along with the discovery of motif combinations. It is developed by the computational System biology Group at UCF.

The identification of DNA regulatory motifs is important for the study of gene regulation. Several hundred computational methods are available for motif identification. Despite their existence, systematically discovery of motifs in large sequence datasets is still suboptimal. The traditional motif finding tools, which were not designed for high-throughput sequencing data, are difficult to handle the large scale ChIP-seq peaks. Most existing de-novo motif discovery tools are monad-based and thus the dyad motifs were completely ignored. Besides, the existing de-novo motif discovery tools are mainly focusing on the identification of individual motifs while it is well known that TFs are always co-working with others to regulate the target gene expression. It is very useful if we can identify the modules besides the motif discovery. Facing these challenges, we proposed a de-novo motif discovery pipeline - SIOMICS 3. Not only does SIOMICS3 identify both monad and dyad motifs with variable lengths from large scale data set, but also it provides motif modules predictions


The following resutls were provided by SIOMICS 2.0
As mentioned in the SIOMICS 3.0 manual , there are :
SIOMICS3 Results:
Result files:
1. X.PWM (predicted motifs in PWM format)
2. X.PWM.TFs (Corresponding TFs for predicted motifs under given E-value cutoff)
This result is only available under Linux since it is based on STAMP and STAMP is not available under Windows
Although we cant' use STAMP standlone tool under Linux, we can use STAMP on-line server to compare the predicted motifs and known motifs in provided database. The online comparison results were provided as X.STAMP.pdf, which is downloaded from STAMP server.
3. X.STAMP.pdf (STAMP comparison details in PDF for predicted motifs)
4. X.mc (Predicted motif combinations)
5. X.tfbs (The TFBSs for predicted motifs)
6. X.trans (The transaction file generated for pattern mining)
7. X.sif (Simple interaction file generated for visualization of TF-TF interaction using cytoscape)
8. Running.log

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click here to download SIOMICS 3.0 software

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SIOMICS 3.0 predictions in 13 mESC TF ChIP-seq