Dual restriction enzyme digest of cationic-gold-coated DNA scaffolds

Modeling of Partial Digest Problem as a Network flows problem

Restriction Site Mapping is one of the interesting tasks in Computational Biology. A DNA strand can be thought of as a string on the letters A, T, C, and G. When a particular restriction enzyme is added to a DNA solution, the DNA is cut at particular restriction sites. The goal of the restriction site mapping is to determine the location of every site for a given enzyme. In partial digest metho...

The Simplified Partial Digest Problem: Hardness and a Probabilistic Analysis

Introduction We study the problem of genome mapping using restriction site analysis. In restriction site analysis, an enzyme cuts a target DNA strand into DNA fragments, and these DNA fragments are used to reconstruct the restriction site locations of the enzyme. Two common approaches are the Double Digest Problem and the Partial Digest Problem. The Double Digest Problem is known to be NP-Compl...

One-tube restriction enzyme digest and fluorescent labeling for restriction endonuclease fingerprinting single-strand conformational polymorphism.

Renewal Theory for Several Patterns

The results presented in this paper were motivated by a study of certain patterns, known as restriction sites, in DNA sequences. DNA sequences can be thought of as finite words over a four-letter alphabet {A, T, G, C}, and restriction sites are (sequence-specific) locations of positions in double-stranded DNA where it is cut by a protein known as a restriction enzyme. See Watson (1977). For exa...

Description of the entire mRNA population by a 3' end cDNA fragment generated by class IIS restriction enzymes.

A novel means of recording the expression status of the total gene population is described. Digestion of cDNA by class IIS restriction enzymes produces a fragment with a poly (A) stretch and a 5' overhang with an unknown sequence. This fragment contains information such as the class IIS enzyme that cuts cDNA nearest to the poly (A) stretch, the sequence of the 5' overhang, and the size of the f...