RAP: a new computer program for de novo identification of repeated sequences in whole genomes

Bioinformatics
Davide CampagnaGiorgio Valle

Abstract

DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats. The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences. The program is freely available for non-profit organizations, upon request to the authors. giorgio.valle@unipd.it The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.

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Citations

Nov 17, 2005·Bioinformatics·Aleksandr MorgulisRicha Agarwala
Feb 20, 2007·Bioinformatics·Minmei HouRobert S Harris
Dec 20, 2007·Bioinformatics·Xuehui LiA Mark Settles
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
Jul 5, 2006·Journal of Bioinformatics and Computational Biology·Simon B Kogan
Jan 16, 2008·BMC Bioinformatics·David EllinghausUte Willhoeft
Dec 5, 2006·BMC Genomics·Ralph T WiedmannJohn W Keele
Dec 21, 2005·Journal of Biomolecular Structure & Dynamics·A FadielA Hamza
Aug 19, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Mateusz JanickiGuojun Yang
Jun 11, 2008·Analytical Biochemistry·Wanjun GuDavid D Pollock
Mar 5, 2008·International Journal of Plant Genomics·Amalia BaroneLuigi Frusciante
Oct 10, 2008·BMC Genomics·Feng YueJijun Tang
Feb 8, 2008·BioTechniques·Sara TodescoAlessandro Vezzi
Aug 9, 2019·International Journal of Molecular Sciences·Simon Orozco-AriasRomain Guyot
Apr 13, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Subhadip KunduAshok Sharma

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