Hybrid Motif Sampler

HMS (hybrid motif sampler) implements a novel computational algorithm specifically designed for transcription factor binding sites (TFBS) motif discovery using ChIP-Seq data. HMS combines stochastic sampling with determinstic greedy search to achieve rapid and accurate motif pattern identification. In addition, it can identify non-ignorable inter-position dependency inside TFBS motifs. The program is written in C++, and both source code and linux executable are availiable for download.

Download program

Download the latest version and the source code of HMS. [March, 2010]

Download datasets

Download ChIP-Seq and ChIP-chip datasets.

Download PSWM

Download position specific weight matrix (PSWM) from de novo motif searching using ChIP-Seq data.


Includes the user manual, manuscript and supplementary material describing HMS.

Update & Bug Log

Log of updates, bugs and fixes. Also has the previous versions of the program.


If you use HMS, please register with us. It helps us to send you updates and bug-fixes.


For bug report, questions or comments, please contact Ming Hu (