Biomedical subjects

P Formanowicz

Publications and source records attributed to P Formanowicz.

4 recordsLinked to original sources

PubMed2004

An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes.

An algorithm is proposed to provide the tool for an automatic resonance assignment of 2D-NOESY spectra of RNA duplexes. The algorithm, based on a certain subproblem of the Hamiltonian path, reduces a number of possible connections between resonances within aromatic and anomeric region of 2D-NOESY spectra. Appropriate pathways between H6/H8 and H1' resonances were obtained by subsequent implementation of experimental data as limiting factors. Predictive power of the algorithm was tested on both experimental and simulated data for RNA and DNA duplexes.

Algorithms↗

PubMed2001

Construction of DNA restriction maps based on a simplified experiment.

MOTIVATION: A formulation of a new problem of the restriction map construction based on a simplified digestion experiment and a development of an algorithm for solving both ideal and noisy data cases of the introduced problem. RESULTS: A simplified partial digest problem and a branch and cut algorithm for finding the solution of the problem.

Algorithms↗

PubMed1999

DNA sequencing with positive and negative errors.

The problem addressed in this paper is concerned with DNA sequencing by hybridization. An algorithm is proposed that solves a computational phase of this approach in the presence of both positive and negative errors resulting from the hybridization experiment. No a priori knowledge of the nature and source of these errors is required. An extensive set of computational experiments showed that the algorithm behaves surprisingly well if only positive errors appear. The general case, where positive and negative errors occur, can be also solved satisfactorily for an error rate up to 10%.

Algorithms↗

PubMed1997

Sequencing by Hybridization with Positive Faults.

The paper is concerned with a computational phase of the sequencing DNA chains by hybridization. It is assumed that positive faults can occur in the hybridization experiment. An approach based on a reduction of the problem to a variant of a Selective Traveling Salesman Problem and an algorithm for solving the latter, have been proposed. The algorithm behaves extremely well, even for a fault rate exceeding 50%.

Journal Article↗