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

Paar, V.; Pavin, Nenad; Rosandić, Marija; Glunčić, Matko; Basar, Ivan; Pezer, Robert; Žinić, Sonja Durajlija

doi:10.1093/bioinformatics/bti072

Cited by 27 publications

(38 citation statements)

References 28 publications

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“…Previously we identified HOR and derived exact consensus lengths (Paar et al 2005) for most of the HOR from Table 1. The 13mer in chromosome 4 is determined here for the first time.…”

Section: Resultsmentioning

confidence: 99%

“…The Key String Algorithm (KSA) was used to obtain HOR copies and consensus HOR. KSA is a simple and effective computational method to detect and investigate HOR in a given genomic sequence (Rosandić et al 2003a, 2003b, Paar et al 2005. KSA could be considered as an extended computational analog of the restriction enzyme method.…”

Section: Methodsmentioning

confidence: 99%

“…The Key String Algorithm (KSA), our new computational method, was shown to be very effective in identifying and analyzing HOR and their structure from human genome assembly Build 35.1 (Rosandić et al 2003a, 2003b, Paar et al 2005.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2006

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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.

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“…Previously we identified HOR and derived exact consensus lengths (Paar et al 2005) for most of the HOR from Table 1. The 13mer in chromosome 4 is determined here for the first time.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

et al. 2006

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“…As a case study, this new method is applied to the following DNA sequences: to human and chim-panzee alpha satellite consensus HORs, to monomeric alpha satellite regions and to no-repeat DNA regions (Table 1 and Supplementary table S1). In these studies the consensus sequences are determined by GRM analysis [25][26][27][28][29][30][31][32][33] of the recent Build 37.2 assembly (Figure 1). First the dinucleotide frequencies in consensus alpha satellites are analyzed (Supplementary table S2).…”

Section: Resultsmentioning

confidence: 99%

Start/stop Codon-like Trinucleotides (CLTs) and Extended Clusters as New Language of DNA

Rosandić¹,

Glunčić²,

Paar³

2011

Croat. Chem. Acta

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Abstract. DNA nucleotide sequences carry genetic information of different kinds, not just coding instructions for protein synthesis. They can play a role, for example, in alternative conformations and gene regulators. The present paper introduces the extended start/stop codon-like trinucleotides (CLTs) for noncoding DNA sequences, based on trinucleotide cluster extension generated by specific single-nucleotide multiplications. Extended cluster analysis gives rise to rich information potential as a "new language" of DNA ("CLT-language"). The analysis of start/stop-CLTs extended clusters provides qualitative and quantitative differentiation and characterization of alpha satellites, as well as of other repetitive and non-repetitive noncoding sequences. As a measure of CLT extension of DNA sequences the extension factor r is introduced. Start/stop CLTs enable a distinction of three segments within alpha satellite, the first and the second as wrapping sequences and the third as a linker. Within a linker there are no start/stop CLTs. On the basis of start/stop-CLTs, it is hypothesized that these noncoding sequences may be involved in the networks of gene regulators. (doi: 10.5562/cca1948)

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“…The KSA framework 48,49,52,53 is based on the use of a short sequence of nucleotides, referred to as key string, which cuts a given genomic sequence at each location of the key string appearing within the sequence. Going along genomic sequence, the lengths of ensuing KSA fragments form KSA length array.…”

Section: Key String Algorithm (Ksa)mentioning

confidence: 99%

Global Repeat Map Method for Higher Order Repeat Alpha Satellites in Human and Chimpanzee Genomes (Build 37.2 Assembly)

Glunčić¹,

Rosandić²,

Jelovina³

et al. 2012

Croat. Chem. Acta

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Abstract. Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to the functional and structural role within centromere they are also a suitable model for evolutionary studies, because of being subject to concerted evolution. The Global Repeat Map (GRM) algorithm is a convenient computational tool to determine consensus repeat units and their exact size within a given genomic sequence, both of monomeric and higher-order (HOR) type. Using GRM, we identify in Build 37.2 assembly fifteen different alpha satellite HORs, three of them novel, not reported previously. In the next step we compute suprachromosomal family classification and CENP-B box / pJ distributions for these HORs. All human alpha satellite sequences originate from one pra-ancestral alpha satellite monomer. For the first time we perform GRM analysis and compare human and chimpanzee alpha satellite HORs for chromosomes 4 and give an evidence that the human and chimpanzee alpha satellites originate from a common ancestor that predated the human-chimpanzee separation. We also compare the codon-like trinucleotide (CLT) extensions of human and chimpanzee chromosome 4. Our results are consistent with the expectation that the alpha satellite HORs in human and chimpanzee have been created after the human-chimpanzee separation.

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

Cited by 27 publications

References 28 publications

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

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

Start/stop Codon-like Trinucleotides (CLTs) and Extended Clusters as New Language of DNA

Global Repeat Map Method for Higher Order Repeat Alpha Satellites in Human and Chimpanzee Genomes (Build 37.2 Assembly)

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