ArticleNucleic acids research2013
Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 36 citations in OpenAlex.
- Article
- Article
- Novel Cascade Alpha Satellite HORs in Orangutan Chromosome 13 Assembly: Discovery of the 59mer HOR-The largest Unit in Primates-And the Missing Triplet 45/27/18 HOR in Human T2T-CHM13v2.0 Assembly.International journal of molecular sciences · 2024Article
- Precise identification of cascading alpha satellite higher order repeats in T2T-CHM13 assembly of human chromosome 3.Croatian medical journal · 2024Article
- Novel Concept of Alpha Satellite Cascading Higher-Order Repeats (HORs) and Precise Identification of 15mer and 20mer Cascading HORs in Complete T2T-CHM13 Assembly of Human Chromosome 15.International journal of molecular sciences · 2024Article
- Efficient genome monomer higher-order structure annotation and identification using the GRMhor algorithm.Bioinformatics advances · 2024Article
- Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly.Scientific reports · 2023Article
- Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution.Life science alliance · 2023Article
- Advances in the computational analysis of SARS-COV2 genome.Nonlinear dynamics · 2021Article
- Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma Breakpoint Family (NBPF) Genes, in Hornerin Exon and in Chromosome 21 Centromere.Progress in molecular and subcellular biology · 2021Article
- Identification of tandem repeat families from long-read sequences of Humulus lupulus.PloS one · 2020Article
- Computational analysis of the SARS-CoV-2 and other viruses based on the Kolmogorov's complexity and Shannon's information theories.Nonlinear dynamics · 2020Article
- Discovery of 33mer in chromosome 21 - the largest alpha satellite higher order repeat unit among all human somatic chromosomes.Scientific reports · 2019Article
- Satellite DNA evolution: old ideas, new approaches.Current opinion in genetics & development · 2018Review
- Regular Higher Order Repeat Structures in Beetle Tribolium castaneum Genome.Genome biology and evolution · 2017Article
- TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.Nucleic acids research · 2017Article
- Periodic power spectrum with applications in detection of latent periodicities in DNA sequences.Journal of mathematical biology · 2016Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of 'magnifying glass' effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.