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In this paper we proposed a new distance computing method for DNA sequences. Given a set of species, the method first codes the DNA sequences of each species into a characteristic vector, and then computes a distance matrix for the set of species based on these characteristic vectors. The distance matrix obtained can be used to construct phylogenetic trees for phylogenetic analysis. Such a method...
Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. In this paper, we incorporate DNA copy number variation data derived from SNP arrays into a computational shrunken model and formalize the detection of copy number variations as a case-control classification problem. By shrinkage, the number of relevant CNVs to disease can be...
Infectious microorganisms represent the causes of many of the most common and dangerous diseases in our modern society. Two major problems exist when tackling the problem of infections: detection and treatment. Here we utilize two distinct nanotechnology platforms to combat these problems. First, we demonstrate a novel detection method for identifying Mycobacterium tuberculosis DNA using rolling circle...
In this study, the RAPD (Random Amplified Polymorphic DNA) technology was used to identify the genotypic variation between the parental strain and the shuffled strain of Streptomyces gilvosporeus. Firstly, RAPD conditions were optimized by orthogonal test. The results were as follows: DNA 60-150 ng, Taq DNA polymerase 1.0-1.5U, primer concentration 0.3-0.4 mmol/L, dNTPs concentration 200-250 μmol/L,...
CYP17 (17α-hydroxylase/17, 20-lyase) has been viewed as a critical enzyme for the biosynthesis of gonadal and adrenal steroids in vertebrates. According to a reported CYP17 gene of Strongylocentrotus purpuratus gene from NCBI, three pairs of primers were designed to clone CYP17 gene of Strongylocentrotus nudus,using RT-PCR. Three fragments were assembled into on contig of 1569bp, including full CDS...
We use the stochastic linearized Poisson-Boltzmann equation to model the fluctuations in nanowire field-effect biosensors due to changes in the orientation of the biomolecules. Different orientations of the biomolecules with respect to the sensor surface due to Brownian motion have different probabilities. The probabilities of the orientations are calculated from their electrostatic free energy. The...
This modeling work examines the critical role of nanowire surface properties in its DNA sensing performance in terms of both signal levels and input dynamic ranges. Such properties include surface charge group density, oxide thickness and oligomer surface density, charges and energetic heterogeneity. The presence of surface charge groups are shown to contribute to additional charge screening. The...
Device-level simulation capabilities have been developed to self-consistently model the Si-nanowire (NW) biosensor systems. Our numerical study demonstrates that by introducing electro-diffusion current flow in the electrolyte solutions, the electrostatic screening of the biological charge can be significantly suppressed; an improvement of the sensed signal strength by >ap10X is indicated. Based...
Biology sequence database search is an important problem for bioinformatics research. The main search software BLAST is based on the BYP algorithm. In BYP, if the length of hit region is set long, it may lose similar appearance. Otherwise, there may be too many r-length regions from Aho-Corasik algorithm. Checking where exists any approximate alignments for the DNA or RNA sequence always spends much...
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