Vladimir Paar

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BACKGROUND Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively(More)
Using our Key String Algorithm (KSA) to analyze Build 35.1 assembly we determined consensus alpha satellite higher-order repeats (HOR) and consensus distributions of CENP-B box and pJalpha motif in human chromosomes 1, 4, 5, 7, 8, 10, 11, 17, 19, and X. We determined new suprachromosomal family (SF) assignments: SF5 for 13mer (2211 bp), SF5 for 13mer (2214(More)
A new key-string segmentation algorithm for identification of alpha satellite DNAs and higher-order repeat (HOR) units was introduced and exemplified. Starting with an initial key string, we determine the dominant key string and HOR. Our key-string algorithm was used to scan the recent GenBank data for human alpha satellite DNA sequence AC017075.8 (193 277(More)
Key string algorithm (KSA) could be viewed as robust computational generalization of restriction enzyme method. KSA enables robust and effective identification and structural analyzes of any given genomic sequences, like in the case of NCBI assembly for human genome. We have developed a method, using total frequency distribution of all r-bp key strings in(More)
MOTIVATION GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from(More)
This article aims at providing a new theoretical insight into the fundamental question of the origin of truncated fractals in biological systems. It is well known that fractal geometry is one of the characteristics of living organisms. However, contrary to mathematical fractals which are self-similar at all scales, the biological fractals are truncated,(More)
AIM To use a novel computational approach, Key-string Algorithm (KSA), for the identification and analysis of arbitrarily large repetitive sequences and higher-order repeats (HORs) in noncoding DNA. This approach is based on the use of key string that plays a role of an arbitrarily constructed "computer enzyme". METHOD A cluster of novel KSA-related(More)
The 21st century has brought important changes in the paradigms of economic development, one of them being a shift toward recognizing knowledge and information as the most valuable commodities of today. The European Union (EU) has been working hard to become the most competitive knowledge-based society in the world, and Croatia, an EU candidate country, has(More)
Much attention has been devoted to identifying genomic patterns underlying the evolution of the human brain and its emergent advanced cognitive capabilities, which lie at the heart of differences distinguishing humans from chimpanzees, our closest living relatives. Here, we identify two particular intragene repeat structures of noncoding human DNA, spanning(More)