A parametric signal processing approach for DNA sequence analysis based on autoregressive (AR) modeling is presented. AR model residual errors and AR model parameters are used as features. The AR residual error analysis indicates a high specificity of coding DNA sequences, while AR feature-based analysis helps distinguish between coding and noncoding DNA sequences. An AR model-based string sear...

DNA computing 1 potentially provides a degree of parallelism far beyond that of conventional silicon-based computers. A number of researchers 2 have experimentally demonstrated DNA computing in solving instances of the satisfiability problems. Self-assembly of DNA nanostructures is theoretically an efficient method of executing parallel computation where information is encoded in DNA tiles and ...

There exists a strong need for a qualitative spatial knowledge representation that is capable of modeling and of reasoning about knowledge of genomic structures. The reasoning component can help to improve the biological plausibility of existing alignment approaches for bacterial genomic DNA sequences, which at present relies exclusively on similarity comparisons on the string level. Genomic DN...

A string matching—andmore generally, sequence matching—algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is better than that of the fastest versions of the Boyer-Moore algorithm. The algorithm retains its efficiency advantages in a wide variety of sequence matching problems...

The promoter region of the chicken adult beta-globin gene contains a sequence of 16 deoxyguanosine residues located at a nucleosome boundary in tissues where the gene is inactive. In definitive erythrocytes that express the beta-globin gene, the nucleosome is displaced, the G-string and adjacent sequences are occupied by sequence-specific DNA-binding proteins, and a nuclease hypersensitive doma...

Two new models for implementing finite state machines with DNA computing are presented. The operations used in both models are simple and easy to implement. Operations include immobilization of DNA strands onto paramagnetic beads, DNA hybridization, DNA ligation and restriction enzyme cleavage. Use of paramagnetic beads greatly reduces performance time and demonstrates DNA chip compatibility of...

String matching is one of most challenging issues in computer science. In this study, a new efficient hybrid string matching algorithm called Atheer was developed. This proposed algorithm is integrated with the excellent properties of three algorithms, namely, the Karp–Rabin, Raita, and Smith algorithms. The Atheer algorithm demonstrated an efficient performance in the number of comparison atte...

Motivated by the recombinant behavior of DNA, Tom Head introduced a scheme for the evolution of formal languages called splicing. We give a simpler proof of the fundamental fact that the closure of a regular language under iterated splicing using a finite number of splicing rules is again regular. We then extend this result in two directions, by incorporating circular strings and by using infin...

A tangle consists of strings properly embedded in a 3-dimensional ball. Tangles have been used to model protein-bound DNA. The protein is represented by the 3D ball and the protein-bound DNA is represented by the strings embedded in the 3D ball. We review tangle analysis of protein-DNA complexes involving three or four segments of DNA. 1. Introduction. An n-string tangle is a three dimensional ...