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HyperMotif:
hypergeometric-based analysis of sequence motifs
 Short
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 hamed.shaterinajafabadi@mail.mcgill.ca.
For other inquiries contact reza.salavati@mcgill.ca.
HyperMotif
Developers:
Hamed Shateri Najafabadi
Reza Salavati
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