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Schmitt et al. (1) raise the concern that circle sequencing (2) may spuriously count information from the same starting molecule multiple times. There are indeed several mechanisms by which multiple final reads produced by the circle-sequencing process could be derived from the same starting molecule, as discussed briefly in the last paragraph of our Results section (2). As Schmitt et al. (1) point out, the extent to which this occurs …
[↵][1]1To whom correspondence should be addressed. E-mail: wpress{at}cs.utexas.edu.
[1]: #xref-corresp-1-1
Synthetic DNA is rapidly emerging as a durable, high-density information storage platform. A major challenge for DNA-based information encoding strategies is the high rate of errors that arise during DNA synthesis and sequencing. Here, we describe the HEDGES (Hash Encoded, Decoded by Greedy Exhaustive Search) error-correcting code that repairs all three basic types of DNA errors: insertions, deletions, and substitutions. HEDGES also converts unresolved or compound errors into substitutions, restoring synchronization for correction via a standard Reed-Solomon outer code that is interleaved across strands. Moreover, HEDGES can incorporate a broad class of user-defined sequence constraints, such as avoiding excess repeats, or too high or too low windowed guanine-cytosine (GC) content. We test our code both via in silico simulations and with synthesized DNA. From its measured performance, we develop a statistical model applicable to much larger datasets. Predicted performance indicates the possibility of error-free recovery of petabyte- and exabyte-scale data from DNA degraded with as much as 10% errors. As the cost of DNA synthesis and sequencing continues to drop, we anticipate that HEDGES will find applications in large-scale error-free information encoding.
Informal verbal interaction is the core matrix for human social life. A mechanism for coordinating this basic mode of interaction is a system of turn-taking that regulates who is to speak and when. Yet relatively little is known about how this system ...
Important and useful to every student of relativity, this book is a unique collection of some 475 problems--with solutions--in the fields of special and general relativity, gravitation, relativistic astrophysics, and cosmology. The problems are expressed in broad physical terms to enhance their pertinence to readers with diverse backgrounds. In their solutions, the authors have attempted to convey a mode of approach to these kinds of problems, revealing procedures that can reduce the labor of calculations while avoiding the pitfall of too much or too powerful formalism. Although well suited for individual use, the volume may also be used with one of the modem textbooks in general relativity.
The windows of observational astronomy have become broader. They now include, along with photons from many decades of the electromagnetic spectrum, extraterrestrial artifacts of other sorts: cosmic rays, meteorites, particles from
the solar wind, samples of the lunar surface, and neutrinos. With gravitational-wave
astronomy, we are on the threshold-or just beyond the threshold-of adding another window; it is a particularly important window because it will
allow us to observe phenomena that cannot be studied adequately by other
means: gravitational collapse, the interiors of supernovae, black holes, short-period
binaries, and perhaps new details of pulsar structure. There is the further possibility that gravitational-wave astronomy will reveal entirely new phenomena-or familiar phenomena in unfamiliar guise-in trying to explain the observations of Joseph Weber.
From the Publisher:
This is the revised and greatly expanded Second Edition of the hugely popular Numerical Recipes: The Art of Scientific Computing. The product of a unique collaboration among four leading scientists in academic research and industry, Numerical Recipes is a complete text and reference book on scientific computing. In a self-contained manner it proceeds from mathematical and theoretical considerations to actual practical computer routines. With over 100 new routines (now well over 300 in all), plus upgraded versions of many of the original routines, this book is more than ever the most practical, comprehensive handbook of scientific computing available today. The book retains the informal, easy-to-read style that made the first edition so popular, with many new topics presented at the same accessible level. In addition, some sections of more advanced material have been introduced, set off in small type from the main body of the text. Numerical Recipes is an ideal textbook for scientists and engineers and an indispensable reference for anyone who works in scientific computing. Highlights of the new material include a new chapter on integral equations and inverse methods; multigrid methods for solving partial differential equations; improved random number routines; wavelet transforms; the statistical bootstrap method; a new chapter on less-numerical algorithms including compression coding and arbitrary precision arithmetic; band diagonal linear systems; linear algebra on sparse matrices; Cholesky and QR decomposition; calculation of numerical derivatives; Pade approximants, and rational Chebyshev approximation; new special functions; Monte Carlo integration in high-dimensional spaces; globally convergent methods for sets of nonlinear equations; an expanded chapter on fast Fourier methods; spectral analysis on unevenly sampled data; Savitzky-Golay smoothing filters; and two-dimensional Kolmogorov-Smirnoff tests. All this is in addition to material on such basic top
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