Super-Secondary structure elements (super-SSEs) are the structurally conserved ensembles of secondary structure elements (SSEs) within a protein. They are of great biological interest. In this work, we present a method to formally represent and mine the sequence order independent super-SSE motifs that occur repeatedly in large data sets of protein structures. We represent a protein structure as...

Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. Overrepresentation of convergent occurrences of motifs in proteins with a common attribute (such as similar subcellular location or a shared interaction partner) provides a feasible means to discover novel occurrences computationally. The SLiMDisc (Short, Linear Motif Di...

Combinatorial Motif Analysis in Yeast Gene Promoters: The Benefits of a Biological Consideration of Motifs. (December 2004) Kevin L. Childs, B.S., University of Michigan; Ph.D., Texas A&M University Chair of Advisory Committee: Dr. Thomas R. Ioerger There are three main categories of algorithms for identifying small transcription regulatory sequences in the promoters of genes, phylogenetic comp...

Abstract The structure of complex networks can be characterized by counting and analysing network motifs. Motifs are small graph structures that occur repeatedly in a network, such as triangles or chains. Recent work has generalized motifs to temporal dynamic data. However, existing techniques do not generalize sequential trajectory data, which represent entities moving through the nodes passen...

In this paper, we consider the problem of extracting multiple unordered short motifs in upstream regions of given genes. Multiple unordered short motifs can be considered as a set of short motifs, say M = {m1, m2, . . . , mk}. For a gene g, if each of the motifs m1, . . . , mk occurs in either the upstream region or its complement of g, the gene g is said to be consistent with M . We have devel...

(received 4 jan 2014, accepted 2 mar 2014) abstract mazandaran, the northern province of iran, as an area with a different climate and political situation in their own special place has been allocated with itself in the history of this land. researchers familiar with the history, culture and art of ancient civilizations, have known this place a good platform for own exploring and searching. the...

Investigation of household electricity usage patterns, and mat- ching the patterns to behaviours, is an important area research given centrality such in addressing needs indu- stry. Additional knowledge behaviours will allow more effective targeting demand side management (DSM) techniques. This paper addresses question as whether a reasonable number meaningful motifs, that each represent regula...

To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs ...