RT Journal
A1 Churakov, Gennady
A1 Zhang, Fengjun
A1 Grundmann, Norbert
A1 Makalowski, Wojciech
A1 Noll, Angela
A1 Doronina, Liliya
A1 Schmitz, Juergen
T1 The multi-comparative 2-n-way genome suite
JF Genome Research 
JO Genome Research 
YR 2020 
FD July 29 
DO 10.1101/gr.262261.120 
SP gr.262261.120 
UL http://genome.cshlp.org/content/early/2020/07/29/gr.262261.120.abstract 
AB 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. Thus, the "2-n-way" software suite is ideal for performing multi-directional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose ~100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.