<![CDATA[BOL: Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences]]> https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences? https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences Tue, 26 Apr 2016 12:18:49 -0500 https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences <![CDATA[Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences]]> Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.

Address of the bookmark: http://bioinformatics.ua.pt/software/smash/

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