To predict alterations in single-strand DNA mobility in non-denaturing electrophoretic gels, Zuker's RNA folding program was modified. Energy files utilized by the LRNA RNA folding algorithm were modified to emulate folding of single-strand DNA. Energy files were modified to disallow G-T base pairing. Stacking energies were corrected for DNA thermodynamics. Constraints on loop nucleotide sequen...

This paper proposes a DNA sticker algorithm for parallel reduction over finite field GF(2 n ). This algorithm is suitable for some specific finite fields defined with trinomials or pentanomials. We use one binary finite field GF(2 163 ) which is recommended by National Institute of Standards and Technology (NIST) to describe the details about our algorithm. The solution space of 2 325 cases cou...

We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc.) combining with the logistic chaotic map to scramble the location and the...

Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circui...

We present a Compression Tool , GenBit Compress”, for genetic sequences based on our new proposed “GenBit Compress Algorithm”. Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better compression results show that GenBit compress algorithm is the best among the remaining Genome compression algorithms for non-repetitive DNA sequences in Genomes. The ...

DNA methylation is an important epigenetic event that effects gene expression during development and various diseases such as cancer. Understanding the mechanism of action of DNA methylation is important for downstream analysis. In the Illumina Infinium HumanMethylation 450K array, there are tens of probes associated with each gene. Given methylation intensities of all these probes, it is neces...

This study proposes use of the DNA genetic artificial fish swarm constant modulus blind equalization algorithm (DNA-G-AFS-CMBEA) to overcome the local convergence of the CMBEA. In this proposed algorithm, after the fusion of the fast convergence of the AFS algorithm and the global search capability of the DNA-G algorithm to drastically optimize the position vector of the artificial fish, the gl...

background and objectives: dna ladder contains dna fragments of different length but with known size, used to determine the size of unknown dna molecules. different dna ladders are available for expected dna length. conserved sequences were selected for design of primers to generate dna fragments of known specific size. materials and methods: in this study, we describe a method by which dna lad...

This paper demonstrates that some practical 3SAT algorithms on conventional computers can be implemented on a DNA computer as a polynomial time breadth first search procedure based only on the fundamental chemical operations identified by Adleman and Lipton’s method. In particular, the MonienSpeckenmeyer algorithm, when implemented on DNA, becomes an time, ! space algorithm, with significant in...

The extraction of DNA strands including a given sequence of bases is a crucial step in the Adleman-Lipton extract model of DNA computing. In this paper, a special type of PCR is presented with a related algorithm which performs a specified extraction from a given pool of DNA double stranded (shortly dsDNA) molecules. This kind of PCR, called Cross Pairing PCR (shortly XPCR) was tested in severa...