{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T11:46:17Z","timestamp":1777117577193,"version":"3.51.4"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2020,5,20]],"date-time":"2020-05-20T00:00:00Z","timestamp":1589932800000},"content-version":"vor","delay-in-days":19,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Tested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ~1 GB, which makes Smash++ feasible to run on present-day standard computers.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giaa048","type":"journal-article","created":{"date-parts":[[2020,5,20]],"date-time":"2020-05-20T07:39:39Z","timestamp":1589960379000},"source":"Crossref","is-referenced-by-count":17,"title":["Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements"],"prefix":"10.1093","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8962-8985","authenticated-orcid":false,"given":"Morteza","family":"Hosseini","sequence":"first","affiliation":[{"name":"IEETA\/DETI, University of Aveiro , Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro,","place":["Portugal"]}]},{"given":"Diogo","family":"Pratas","sequence":"additional","affiliation":[{"name":"IEETA\/DETI, University of Aveiro , Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro,","place":["Portugal"]},{"name":"Department of Virology, University of Helsinki , Haartmaninkatu 3, 00014 Helsinki,","place":["Finland"]}]},{"given":"Burkhard","family":"Morgenstern","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, University of G\u00f6ttingen , Goldschmidtstr. 1, 37077 G\u00f6ttingen,","place":["Germany"]},{"name":"G\u00f6ttingen Center of Molecular Biosciences (GZMB) , Justus-von-Liebig-Weg 11, 37077 G\u00f6ttingen,","place":["Germany"]}]},{"given":"Armando J","family":"Pinho","sequence":"additional","affiliation":[{"name":"IEETA\/DETI, University of Aveiro , Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2020,5,20]]},"reference":[{"issue":"4","key":"2024111606404933000_bib1","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1016\/j.molcel.2015.05.004","article-title":"High-throughput sequencing technologies","volume":"58","author":"Reuter","year":"2015","journal-title":"Mol Cell"},{"issue":"5","key":"2024111606404933000_bib2","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1094\/PHYTO-07-18-0257-RVW","article-title":"High throughput sequencing for plant virus detection and discovery","volume":"109","author":"Villamor","year":"2019","journal-title":"Phytopathology"},{"issue":"1","key":"2024111606404933000_bib3","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a026849","article-title":"High throughput sequencing and assessing disease risk","volume":"9","author":"Rego","year":"2019","journal-title":"Cold Spring Harb Perspect Med"},{"key":"2024111606404933000_bib4","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/978-1-4939-7463-4_9","article-title":"Genome rearrangement analysis: cut and join genome rearrangements and gene cluster preserving approaches","volume-title":"Comparative Genomics","author":"Hartmann","year":"2018"},{"key":"2024111606404933000_bib5","doi-asserted-by":"crossref","DOI":"10.1093\/med\/9780199329007.001.0001","volume-title":"Gardner and Sutherland's Chromosome Abnormalities and Genetic Counseling. 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