Salavati Lab


Institute of Parasitology


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HyperMotif: hypergeometric-based analysis of sequence motifs




HyperMotif2Short linear motifs constitute an important group of functional elements at the level of DNA, RNA, and protein. At the level of DNA and RNA, the most important class of linear motifs encompasses cis-regulatory elements that are recognized and bound by trans-acting elements. At the protein level, short linear motifs are involved in a variety of processes, such as mediating protein-protein interactions, interaction with ligand at protein active site, mediating enzymatic reactions, and modulating protein activity via post-translational modifications. Functional elements often show a non-random pattern of distribution among defined groups of genes and proteins. For example, cis-regulatory elements are over-represented in certain groups of genes if genes are clustered based on co-expression. As another example, signature peptides of protein active sites are over-represented among proteins that have similar molecular functions. Therefore, by finding motifs that are over-represented in a particular group of genes or proteins, we can identify functional sequence elements.


HyperMotif is a package that facilitates identification of group-specific short linear motifs. The programs within this package implement the concept of finding over-represented motifs based on tests of hypergeometric distribution. HyperMotif provides the flexibility to search both nucleic acid and protein sequences for identification of functional sequence motifs. Furthermore, this package allows prediction of protein/gene categories based on the discovered short linear motifs.


For bug reports and usage questions or suggestions contact For other inquiries contact


HyperMotif Developers:

Hamed Shateri Najafabadi

Reza Salavati






Reza Salavatiís profile at McGill

Last updated on 6/5/2011 11:22:25 PM