Method of predicting Splice Sites based on signal interactions

BACKGROUND: Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. RESULTS: According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. CONCLUSION: Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. REVIEWERS: This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand

Complexity of diameter on AT-free graphs is linear

We develop a linear time algorithm for finding the diameter of an asteroidal triple-free (AT-free) graph. Furthermore, we update the definition of polar pairs and develop new properties of polar pairs for (weak) dominating pair graphs. We prove that the problem of computing a simplicial vertex in a general graph can be accomplished in O(n^2) based on an existing reduction to the problem of finding diameter in an AT-free graph. We improve the best-known run-time complexities of several graph theoretical problems

Routing and Wavelength Assignment (RWA) with Power Considerations In All- Optical Wavelength-Routed Networks

Routing and wavelength assignment (RWA) is an important problem that arises in wavelength division multiplexed (WDM) optical networks. Previous studies have solved many variations of this problem under the assumption of perfect conditions regarding the power of a signal. In this paper, we investigate this problem while allowing for degradation of routed signals by components such as taps, multiplexers, and fiber links. We assume that optical amplifiers are preplaced. We investigate the problem of routing the maximum number of connections while maintaining proper power levels. The problem is formulated as a mixed-integer nonlinear program and two-phase hybrid solution approaches employing two different heuristics are develope

Wireless Communication in Data Centers: A Survey

Data centers (DCs) is becoming increasingly an integral part of the computing infrastructures of most enterprises. Therefore, the concept of DC networks (DCNs) is receiving an increased attention in the network research community. Most DCNs deployed today can be classified as wired DCNs as copper and optical fiber cables are used for intra- and inter-rack connections in the network. Despite recent advances, wired DCNs face two inevitable problems; cabling complexity and hotspots. To address these problems, recent research works suggest the incorporation of wireless communication technology into DCNs. Wireless links can be used to either augment conventional wired DCNs, or to realize a pure wireless DCN. As the design spectrum of DCs broadens, so does the need for a clear classification to differentiate various design options. In this paper, we analyze the free space optical (FSO) communication and the 60 GHz radio frequency (RF), the two key candidate technologies for implementing wireless links in DCNs. We present a generic classification scheme that can be used to classify current and future DCNs based on the communication technology used in the network. The proposed classification is then used to review and summarize major research in this area. We also discuss open questions and future research directions in the area of wireless DCs

Design Of An All-Optical WDM Lightpath Concentrator

A design of a nonblocking, all-optical lightpath concentrator using wavelength exchanging optical crossbars and WDM crossbar switches is presented. The proposed concentrator is highly scalable, cost-efficient, and can switch signals in both space and wavelength domains without requiring a separate wavelength conversion stage

Selection Of Switching Sites In All-Optical Network Topology Design

In this paper, we consider the problem of topology design for both unprotected and one-link protected all-optical networks. We investigate the problem of selecting switching sites to minimize total cost of the network. The cost of an optical network is expressed as a sum of three main factors: the site cost, the link cost, and the switch cost. For unprotected networks with linear cost model, we present a mixed integer linear programming (MILP) formulation of the problem. We also present an efficient heuristic to approximate the solution. The experimental results show good performance of the linear cost model heuristic. In 16% of the experiments with 10 nodes network topologies, the linear cost model heuristic had no error. Moreover, for 54% and 86% of the experiments with 10 nodes network topologies, the linear cost model heuristic’s solution is within 2% and 5% of its optimal value respectively. Finally, we extend our approach to one-link protected networks, and present an efficient survivable heuristic, and representative experimental results