Motivation k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations ...

The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we pe...

Chi and Mendel [I], [9] analyzed the performance of the minimum-variance deconvolution (MVD). In this correspondence, a further analysis of the performance of the MVD filter is presented. We show that the MVD filter performs like an inverse filter and a whitening filter as SNR + 00, and like a matched filter as SNR + 0. The estimation error e (k) of the MVD filter is colored noise, but it becom...

The projection filter is an approximate nonlinear filter based on orthogonal projection in the tangent space of a manifold of densities. The Riemannian metric used is the Fisher information metric. In this paper it is shown that if one uses Gaussian densities the projection filter equals a McShane-Fisk-Stratonovich version of the socalled Assumed Density Filter.

Traditionally, direct implementation of a K-tap FIR filter requires K multiply-and-accumulate (MAC) blocks, which are expensive to implement in FPGA due to logic complexity and resource usage. To resolve this issue, we first present DA, which is a architecture without multiplier. This paper implements the DA architecture. This architecture is applicable to only one type of filter Coefficients i...

The selectivity filter of K(+) channels is conserved throughout all kingdoms of life. Carbonyl groups of highly conserved amino acids point toward the lumen to act as surrogates for the water molecules of K(+) hydration. Ion conductivity is abrogated if some of these carbonyl groups flip out of the lumen, which happens (i) in the process of C-type inactivation or (ii) during filter collapse in ...

A two-stage state and parameter estimation algorithm for linear systems has been developed. Stage 1 uses a stochastic approximation method for state estimation, while stage 2 considers parameter estimation through a linear Kalman filter. These two stages are conpled in a bootstrap manner. The algorithm is computationally much simpler than the usual extended Kalman filter. A fourth-order numeric...

Recent results in compressed sensing or compressive sampling suggest that a relatively small set of measurements taken as the inner product with universal random measurement vectors can well represent a source that is sparse in some fixed basis. By adapting a deterministic, non-universal and structured sensing device, this paper presents results on using the annihilating filter to decode the in...