Biomedical subjects

Nenad Pavin

Publications and source records attributed to Nenad Pavin.

4 recordsLinked to original sources

PubMed2006

CENP-B box and pJalpha sequence distribution in human alpha satellite higher-order repeats (HOR).

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 bp), SF2 for 11mer (1869 bp), SF1 for 18mer (3058 bp), SF3 for 12mer (2047 bp), SF3 for 14mer (2379 bp), and SF5 for 17mer (2896 bp) in chromosomes 4, 5, 8, 10, 11, 17, and 19, respectively. In chromosome 5 we identified SF5 13mer without any CENP-B box and pJalpha motif, highly homologous (96%) to 13mer in chromosome 19. Additionally, in chromosome 19 we identified new SF5 17mer with one CENP-B box and pJalpha motif, aligned to 13mer by deleting four monomers. In chromosome 11 we identified SF3 12mer, homologous to 12mer in chromosome X. In chromosome 10 we identified new SF1 18mer with eight CENP-B boxes in every other monomer (except one). In chromosome 4 we identified new SF5 13mer with CENP-B box in three consecutive monomers. We found four exceptions to the rule that CENP-B box belongs to type B and pJalpha motif to type A monomers.

Algorithms↗

PubMed2006

Min-protein oscillations in Escherichia coli with spontaneous formation of two-stranded filaments in a three-dimensional stochastic reaction-diffusion model.

We introduce a three-dimensional stochastic reaction-diffusion model to describe MinD/MinE dynamical structures in Escherichia coli. This model spontaneously generates pole-to-pole oscillations of the membrane-associated MinD proteins, MinE ring, as well as filaments of the membrane-associated MinD proteins. Experimental data suggest MinD filaments are two-stranded. In order to model them we assume that each membrane-associated MinD protein can form up to three bonds with adjacent membrane-associated MinD molecules and that MinE induced hydrolysis strongly depends on the number of bonds MinD has established.

Adenosine Triphosphatases↗

PubMed2004

ColorHOR--novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome.

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 known sequences. RESULTS: We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.

Algorithms↗

PubMed2003

Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA.

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 methods was introduced and developed on the basis of a combination of computations on a very modest scale, by eye inspection and graphical display of results of analysis. Sequence analysis software was developed, containing seven programs for KSA-related analyses. This approach was demonstrated in the case study of alpha satellites and HORs in the human genetic sequence AC017075.8 (193277 bp) from the centromeric region of human chromosome 7. The KSA segmentation method was applied by using DCCGTTT, GTA, and TTTC key strings. RESULTS: Fifty-five copies of 2734-bp 16mer HORs were identified and investigated, and a start-string TTTTTTAAAAA was identified. The HOR-matrix was constructed and employed for graphical display of mutations. KSA identification of HORs in AC017075.8 was compared with that of RepeatMasker and Tandem Repeat Finder, which identified alpha monomers in AC017075.8, but not the HORs. On the basis of KSA study, the centromere folding was described as an effect of HORs and super-HORs (3 x 2734 bp) in AC017075.8. The following novel computational KSA-based methods, easy-to-use and intended for computational "pedestrians", were demonstrated: color-HOR diagram, KSA-divergence method, 171-bp subsequence-convergence diagram, and total frequency distribution of the key-string subsequence lengths. The results were supplemented by Fast Fourier Transform, employing a novel mapping of symbolic genomic sequence into a numerical sequence. CONCLUSION: The KSA approach offers a simple and robust framework for a wide range of investigations of large repetitive sequences and HORs, involving a very modest scope of computations that can be carried out by using a PC. As the KSA method is HOR-oriented, the identification of HORs is even easier than the identification of underlying alpha monomer itself. This approach provides an easy identification of point mutations, insertions, and deletions, with respect to consensus. This may be useful in a wide range of investigations and applied in forensic medicine, medical diagnosis of malignant diseases, biological evolution, and paleontology.

Algorithms↗