Ramakrishna Ramaswamy

Prediction of probable genes by Fourier analysis of genomic sequences

MOTIVATION The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA. RESULT The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative-height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature is utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application. AVAILABILITY A computer program GeneScan which locates coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request.

Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation

MOTIVATION Repetitive DNA sequences, besides having a variety of regulatory functions, are one of the principal causes of genomic instability. Understanding their origin and evolution is of fundamental importance for genome studies. The identification of repeats and their units helps in deducing the intra-genomic dynamics as an important feature of comparative genomics. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length. RESULTS The Spectral Repeat Finder program circumvents these problems by using a discrete Fourier transformation to identify significant periodicities present in a sequence. The specific regions of the sequence that contribute to a given periodicity are located through a sliding window analysis, and an exact search method is then used to find the repetitive units. Efficient and complete detection of repeats is provided together with interactive and detailed visualization of the spectral analysis of input sequence. We demonstrate the utility of our method with various examples that contain previously unannotated repeats. A Web server has been developed for convenient access to the automated program. AVAILABILITY The Web server is available at http://www.imtech.res.in/raghava/srf and http://www2.imtech.res.in/raghava/srf

Strange Nonchaotic Attractors

Aperiodic dynamics which is nonchaotic is realized on Strange Nonchaotic Attractors (SNAs). Such attractors are generic in quasiperiodically driven nonlinear systems, and like strange attractors, are geometrically fractal. The largest Lyapunov exponent is zero or negative: trajectories do not show exponential sensitivity to initial conditions. In recent years, SNAs have been seen in a number of diverse experimental situations ranging from quasiperiodically driven mechanical or electronic systems to plasma discharges. An important connection is the equivalence between a quasiperiodically driven system and the Schrodinger equation for a particle in a related quasiperiodic potential, showing a correspondence between the localized states of the quantum problem with SNAs in the related dynamical system. In this review we discuss the main conceptual issues in the study of SNAs, including the different bifurcations or routes for the creation of such attractors, the methods of characterization, and the nature of dynamical transitions in quasiperiodically forced systems. The variation of the Lyapunov exponent, and the qualitative and quantitative aspects of its local fluctuation properties, have emerged as an important means of studying fractal attractors, and this analysis finds useful application here. The ubiquity of such attractors, in conjunction with their several unusual properties, suggests novel applications.

Adaptive control in nonlinear dynamics

Abstract We extend an adaptive control algorithm recently suggested by Huberman and Lumer to multi-parameter and higher- dimensional nonlinear systems. This control mechanism is remarkably effective in returning a system to its original dynamics after a sudden perturbation in the system parameters changes the dynamical behaviour. We find that in all cases, the recovery time is linearly proportional to the inverse of control stiffness (for small stiffness). In higher dimensions there is an additional optimization problem since increasing stiffness beyond a certain value can retard recovery. The control of fixed point dynamics in systems capable of a wide variety of dynamical behaviour is demonstrated. We further suggest methods by which periodic motion such as limit cycles can be adaptively controlled, and demonstrate the robustness of the procedure in the presence of (additive) background noise.

Intermittency Route to Strange Nonchaotic Attractors

Strange nonchaotic attractors (SNA) arise in quasiperiodically driven systems in the neighborhood of a saddle-node bifurcation whereby a strange attractor is replaced by a periodic (torus) attractor. This transition is accompanied by Type-I intermittency. The largest nontrivial Lyapunov exponent

Universal occurrence of the phase-flip bifurcation in time-delay coupled systems

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Pairwise balance and invariant measures for generalized exclusion processes

is a good order parameter for this route from chaos to SNA to periodic motion: the signature is distinctive and unlike that for other routes to SNA. In particular,

Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER.

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miRNA-regulated dynamics in circadian oscillator models

changes sharply at the SNA to torus transition, as does the distribution of finite-time or

Spectral signatures of the diffusional anomaly in water

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