Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

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).

Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification

“…Our studies in detecting and analyzing repetitive sequences in genome sequences from NCBI assembly (www.ncbi.nlm.nih.gov/mapview/) are performed using GRM method (Rosandić et al, 2003a,b;Paar et al, 2005;Paar et al, 2011a,b;Glunčić and Paar, 2012;Rosandić et al, 2013 ).…”

New Tools for Hop Cytogenomics: Identification of Tandem Repeat Families from Long-Read Sequences ofHumulus lupulus

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Regular higher order repeat structures in beetleTribolium castaneumgenome

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