iTriplet, a rule-based nucleic acid sequence motif finder

<p>Abstract</p> <p>Background</p> <p>With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing.</p> <p>Results</p> <p>We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay.</p> <p>Conclusion</p> <p>iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.</p

FEA simulation of the biomechanical structure overload in the university campus planting

FEM investigation of the branch collapse is provided for the huge healthy chestnut tree. Strong wind gust (24 m/s) is assumed. Thus, simulation has as engineering so methodic value to improve the FEM-teaching of students. The geometry was recovered by the photos and sketches. It includes roots, trunk, branch and conditional crown. Static simulation is provided both in the linear formulation and in the geometrically nonlinear one. Branch under109 goes bending with a moderate portion of the twisting. Near uniform stress dispensation is stated along the branch. There are no stress concentrators at all. The trunk-branch junction is steady enough and self-optimized. The branch has grown with the implementation of the idea of „equal-strength console”. Transforming of the branch section provides constant stress level along the branch. Collapse is caused by a severe accidental wind gust. Work stresses have exceeded twice the allowable level (16 MPa) along the main part of the branch. The tree should be taken as an example of an effective bionic design for the load-bearing system. Simulation confirms the effect of self-reinforcing during tree growth. Tree simulation may be methodologically useful. It is understandable and interesting for students