Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press The multi-comparative 2-n-way genome suite Gennady Churakov*,1†, Fengjun Zhang1†, Norbert Grundmann2, Wojciech Makalowski2, Angela Noll1,3, Liliya Doronina1, and Jürgen Schmitz*,1 1Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany 2Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany 3current address: Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany *Corresponding authors:
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[email protected] †Authors contributed equally Running title: 2-n-way genome analyzer Keywords: Genome aligner, 2-n-way, orthology finder, transposable elements, retrophylogenomics, intron loss, insertion polymorphism 1 Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite is comprised of two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, where user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups.