Andrzej K. Brodzik

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Alignment of DNA segments containing repetitive nucleotide base patterns is an important task in several genomics applications, including DNA sequencing, DNA fingerprinting, pathogen detection, and gene finding. One of the most efficient procedures used for this task is the cross correlation method. The main computations of the procedure are the discrete(More)
MOTIVATION One of the main tasks of DNA sequence analysis is identification of repetitive patterns. DNA symbol repetitions play a key role in a number of applications, including prediction of gene and exon locations, identification of diseases, reconstruction of human evolutionary history and DNA forensics. RESULTS A new approach towards identification of(More)
In this letter, closed-form expressions for the discrete Fourier transform (DFT) of a finite chirp are derived. It is shown that when the normalized chirp rate is coprime with the chirp length, then the DFT of a finite chirp is again a finite chirp with magnitude, chirp rate, and carrier frequency appropriately scaled. In particular, when the normalized(More)
We present a new algorithm for image restoration in limited-angle chromotomography. The algorithm is a generalization of the technique considered previously by the authors, based on a hybrid of a direct method of inversion and the iterative method of projections onto convex sets. The generalization is achieved by introducing a new object domain constraint.(More)
In this work we focus on the relationship between the Dempster-Shafer (DS) and Bayesian evidence accumulation. While it is accepted that the DS theory is, in a certain sense, a generalization of the probability theory, the approaches vary in several important respects, including the treatment of uncertain information and the way the evidence is combined,(More)
This work describes an M<sup>2</sup> &#x00D7; M Zak space construction of new zero correlation zone polyphase sequence sets, of sequence length M<sup>3</sup> and set size M, with all-zero cross-correlation. The construction includes the sets with (M-1)-point, (T<sub>2</sub>M-1)-point and (M<sup>2</sup> -1)-point zero auto correlation zone, where(More)
Availability of DNA data is growing roughly at the rate specified by Moore's law. In many molecular biology applications this data must be compared with a reference sequence, either to establish similarity of genomes or to identify functionally homologous subsequences. Current approaches based on pair-wise sequence alignments are computationally expensive(More)
General conditions are derived for an (N=KL<sup>2</sup>)-point discrete chirp with chirp rate a and carrier frequency b to have minimal support on the LtimesKL Zak transform lattice. Earlier, it has been shown that when the normalized chirp parameters amacr= aK, amacr= aK <sup>2</sup>, and 2bmacr = 2bK are integers, the last two of the same parity, then the(More)