N-gram analysis of 970 microbial organisms reveals presence of biological language models

<p>Abstract</p> <p>Background</p> <p>It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word usage indicative of authors or topics, and that the algorithms originally developed for natural language processing may therefore be applied to genome sequences to draw biologically relevant conclusions. Following this approach of 'biological language modeling', statistical n-gram analysis has been applied for comparative analysis of whole proteome sequences of 44 organisms. It has been shown that a few particular amino acid n-grams are found in abundance in one organism but occurring very rarely in other organisms, thereby serving as genome signatures. At that time proteomes of only 44 organisms were available, thereby limiting the generalization of this hypothesis. Today nearly 1,000 genome sequences and corresponding translated sequences are available, making it feasible to test the existence of biological language models over the evolutionary tree.</p> <p>Results</p> <p>We studied whole proteome sequences of 970 microbial organisms using n-gram frequencies and cross-perplexity employing the Biological Language Modeling Toolkit and Patternix Revelio toolkit. Genus-specific signatures were observed even in a simple unigram distribution. By taking statistical n-gram model of one organism as reference and computing cross-perplexity of all other microbial proteomes with it, cross-perplexity was found to be predictive of branch distance of the phylogenetic tree. For example, a 4-gram model from proteome of <it>Shigellae flexneri 2a</it>, which belongs to the <it>Gammaproteobacteria </it>class showed a self-perplexity of 15.34 while the cross-perplexity of other organisms was in the range of 15.59 to 29.5 and was proportional to their branching distance in the evolutionary tree from <it>S. flexneri</it>. The organisms of this genus, which happen to be pathotypes of <it>E.coli</it>, also have the closest perplexity values with <it>E. coli.</it></p> <p>Conclusion</p> <p>Whole proteome sequences of microbial organisms have been shown to contain particular n-gram sequences in abundance in one organism but occurring very rarely in other organisms, thereby serving as proteome signatures. Further it has also been shown that perplexity, a statistical measure of similarity of n-gram composition, can be used to predict evolutionary distance within a genus in the phylogenetic tree.</p

Monolithic narrow-band active inductors using suspended membrane passive components on silicon substrate

In this paper 8.8 GHz monolithic narrow-band active inductors based on the DIMES-03 silicon bipolar process are reported. Substrate losses have been reduced using micromachined suspended membrane inductors and capacitors. Consequently, higher working frequencies and lower power consumption, than those obtainable using a standard bipolar process, have been realized. Better noise performance is predicted. The results are particularly attractive in low power and low noise circuits

Improving Power Transmission Efficiency and Reliability through Hardware/Software Co- Design

Abstract — The transmission systems of tomorrow must incorporate advanced hardware and software technologies to increase safe utilization of existing facilities to increase reliable long-distance power transfer. However, while hardware technologies can provide the muscle for improved transmission system capabilities, software technologies are also needed to provide the intelligence to use these hardware technologies safely, securely, and effectively. To prevent system failures, future transmission systems must incorporate a combination of advanced hardware and software technologies to increase the safe utilization of existing facilities to increase reliable longdistance power transfer. Improvements are also needed in system-wide monitoring and distributed computer-based control to determine and react to system conditions quickly. Technologies such as these can protect the grid not only against traditional threats to reliability (such as storms and other natural events), but also against deliberate disruptions. Employing robust transmission controllers effectively requires a close development relationship between power electronics engineers and computer scientists such that the hardware development, algorithm development, system assessment, and software development are coordinated to ensure optimal performance. This paper describes these activities at the University o

A figure of merit for the high-frequency noise behavior of bipolar-transistors

A new figure of merit for high-frequency noise behavior for use in the evaluation and development of bipolar silicon process technology is introduced. Basic low noise design rules for optimum transistor biasing and emitter scaling are proposed