In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary relationship accurately depends on the model of sequence evolution, the substitution rate, divergence times and the method used to infer phylogenetic history. A...

Comprehensive sequence-function mapping involves detailing the fitness contribution of every possible single mutation to a gene by comparing the abundance of each library variant before and after selection for the phenotype of interest. Deep sequencing of library DNA allows frequency reconstruction for tens of thousands of variants in a single experiment, yet short read lengths of current seque...

A de Bruijn sequence is a circular binary string of length 2n that contains each binary string of length n exactly once as a substring. A maximum-density de Bruijn sequence is a circular binary string of length ( n

Cyclotomic constructions are given for several infinite families of even length binary sequences which have low negaperiodic autocorrelation. It appears that two of the constructions have asymptotic Merit Factor 6.0 which is very high. Mappings from periodic to negaperiodic autocorrelation are also discussed.

A unified framework is applied to solving various sequence comparison problems for run-length encoded strings. All of these algorithms take O(min{mn′,m′n}) time and O(max{m,n}) space, for two strings of lengths m and n, with m′ and n′ runs, respectively. We assume the linear-gap model and make no assumption on the scoring matrices, which maximizes the applicability of these algorithms. The trac...

To every word w is associated a sequence Gw built by computing at each position i the length of its longest palindromic suffix. This sequence is then used to compute the palindromic defect of a finite word w defined by D(w) = |w| + 1 − |Pal(w)| where Pal(w) is the set of its palindromic factors. In this paper we exhibit some properties of this sequence and introduce the problem of reconstructin...

The use of maximum length sequence analysis (MLSA) with rapid click rates may be of clinical value in newborn hearing screening because a greater number of individual responses can be signal averaged without adding to test time. To examine the potential clinical value of MLSA in newborn screening, auditory brainstem responses (ABRs) from 50 premature newborns were studied. ABRs were acquired wi...

A MASH digital delta–sigma modulator (DDSM) is analyzed mathematically. It incorporates first-order error feedback modulators (EFM) which include prime modulus quantizers to guarantee a minimum sequence length . The purpose of this analysis is to calculate the exact sequence length of the aforementioned MASH DDSM. We show that the sequence length for an th-order member of this modulator family ...

Background: Dense granule antigens (GRA antigens) of Toxoplasma gondii induce strong antibody response in humans and are considered as useful diagnostic antigens. Previous studies reported expression of amino terminal GRA8 protein in fusion with large tags such as glutathione-S-transferase. The present study aimed to produce soluble full length immunogenic GRA8 in bacteria. Methods: GRA8 comple...

Based on 3-D elasticity approach, differential quadrature method (DQM) in axial direction is adopted along with Globalized Nelder–Mead (GNM) algorithm to optimize the stacking sequence of a laminated cylindrical shell. The anisotropic cylindrical shell has finite length with simply supported boundary conditions. The elasticity approach, combining the state space method and DQM is used to obtain...