Better prediction of protein contact number using a support vector regression analysis of amino acid sequence

Background: Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C-beta atoms in other residues within a sphere around the C-beta atom of the residue of interest. Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. In this study, we provide a more accurate contact number prediction method from protein primary sequence. Results: We predict contact number from protein sequence using a novel support vector regression algorithm. Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient between predicted and observed contact numbers of 0.70, which outperforms previously achieved accuracies. Including additional information about sequence weight and amino acid composition further improves prediction accuracies significantly with the correlation coefficient reaching 0.73. If residues are classified as being either contacted or non-contacted, the prediction accuracies are all greater than 77%, regardless of the choice of classification thresholds. Conclusion: The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary sequence and higher order consecutive protein structural and functional properties.

SVMtm: Support vector machines to predict transmembrane segments

A new method has been developed for prediction of transmembrane helices using support vector machines. Different coding schemes of protein sequences were explored, and their performances were assessed by crossvalidation tests. The best performance method can predict the transmembrane helices with sensitivity of 93.4% and precision of 92.0%. For each predicted transmembrane segment, a score is given to show the strength of transmembrane signal and the prediction reliability. In particular, this method can distinguish transmembrane proteins from soluble proteins with an accuracy of similar to99%. This method can be used to complement current transmembrane helix prediction methods and can be Used for consensus analysis of entire proteomes . The predictor is located at http://genet.imb.uq.edu.au/predictors/ SVMtm. (C) 2004 Wiley Periodicals, Inc.

Ross River virus disease in Australia, 1886-1998, with analysis of risk factors associated with outbreaks

Ross River virus (RE) is a mosquito-borne arbovirus responsible for outbreaks of polyarthritic disease throughout Australia. To better understand human and environmental factors driving such events, 57 historical reports oil RR Outbreaks between 1896 and 1998 were examined collectively. The magnitude, regularity, seasonality, and locality of outbreaks were found to be wide ranging; however, analysis of climatic and tidal data highlighted that environmental conditions let differently ill tropical, arid, and temperate regions. Overall, rainfall seems to be the single most important risk factor, with over 90% of major outbreak locations receiving higher than average rainfall in preceding mouths. Many temperatures were close to average, particularly in tropical populations; however, in arid regions, below average maximum temperatures predominated, and ill southeast temperate regions, above average minimum temperatures predominated. High spring tides preceded coastal Outbreaks, both in the presence and absence of rainfall, and the relationship between rainfall and the Southern Oscillation Index and Lit Nina episodes suggest they may be useful predictive tools, but only ill southeast temperate regions. Such heterogeneity predisposing outbreaks supports the notion that there are different RE epidemiologies throughout Australia but also Suggests that generic parameters for the prediction and control of outbreaks are of limited use at a local level.

Eph/Ephrin memhrane proteins: A mammalian expression vector pTIg-BOS-Fc allowing rapid protein purification

There is an urgent need for high purity, single chain, fully functional Eph/ephrin membrane proteins. This report outlines the pTIg-BOS-Fc vector and purification approach resulting in rapid increased production of fully functional single chain extracellular proteins that were isolated with high purity and used in structure-function analysis and pre-clinical studies.

Molecular systematics of the Philippine malaria vector Anopheles flavirostris

Allozyme and molecular sequence data from the malaria vector Anopheles flavirostris (Ludlow) (Diptera: Culicidae) were analysed from 34 sites throughout the Philippines, including the type locality, to test the hypothesis that this taxon is a single panmictic species. A finer-scaled allozyme study, of mainly Luzon samples, revealed no fixed genetic differences in sympatric sites and only low levels of variation. We obtained data from partial sequences for the internal transcribed spacer 2 (ITS2) (483 bp), the third domain (D3) (330 bp) of the 28S ribosomal DNA subunit and cytochrome c oxidase subunit I (COI) of mitochondrial DNA (261 bp). No sequence variation was observed for ITS2, only a one base pair difference was observed between Philippine and Indonesian D3 sequences and An. flavirostris sequences were unique, confirming their diagnostic value for this taxon. Sixteen COI haplotypes were identified, giving 25 parsimony informative sites. Neighbour-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian phylogenetic analysis of COI sequences for An. flavirostris and outgroup taxa revealed strong branch support for the monophyly of An. flavirostris, thus confirming that Philippine populations of this taxon comprise a single separate species within the Minimus Subgroup of the Funestus Group. Variation in the behaviour of An. flavirostris is likely to be intraspecific rather than interspecific in origin. © 2006 The Royal Entomological Society.

Stability for parametric implicit vector equilibrium problems

In this paper, we consider a class of parametric implicit vector equilibrium problems in Hausdorff topological vector spaces where a mapping f and a set K are perturbed by parameters is an element of and lambda respectively. We establish sufficient conditions for the upper semicontinuity and lower semicontinuity of the solution set mapping S : Lambda(1) x A(2) -> 2(X) for such parametric implicit vector equilibrium problems. (c) 2005 Elsevier Ltd. All rights reserved.

Motion vector encryption in multimedia streaming

Streaming video application requires high security as well as high computational performance. In video encryption, traditional selective algorithms have been used to partially encrypt the relatively important data in order to satisfy the streaming performance requirement. Most video selective encryption algorithms are inherited from still image encryption algorithms, the encryption on motion vector data is not considered. The assumption is that motion vector data are not as important as pixel image data. Unfortunately, in some cases, motion vector itself may be sufficient enough to leak out useful video information. Normally motion vector data consume over half of the whole video stream bandwidth, neglecting their security may be unwise. In this paper, we target this security problem and illustrate attacks at two different levels that can restore useful video information using motion vectors only. Further, an information analysis is made and a motion vector information model is built. Based on this model, we describe a new motion vector encryption algorithm called MVEA. We show the experimental results of MVEA. The security strength and performance of the algorithm are also evaluated.

Performance analysis of multi-radio AODV in hybrid wireless mesh networks

Wireless Mesh Networks (WMNs), based on commodity hardware, present a promising technology for a wide range of applications due to their self-configuring and self-healing capabilities, as well as their low equipment and deployment costs. One of the key challenges that WMN technology faces is the limited capacity and scalability due to co-channel interference, which is typical for multi-hop wireless networks. A simple and relatively low-cost approach to address this problem is the use of multiple wireless network interfaces (radios) per node. Operating the radios on distinct orthogonal channels permits effective use of the frequency spectrum, thereby, reducing interference and contention. In this paper, we evaluate the performance of the multi-radio Ad-hoc On-demand Distance Vector (AODV) routing protocol with a specific focus on hybrid WMNs. Our simulation results show that under high mobility and traffic load conditions, multi-radio AODV offers superior performance as compared to its single-radio counterpart. We believe that multi-radio AODV is a promising candidate for WMNs, which need to service a large number of mobile clients with low latency and high bandwidth requirements.