2018
DOI: 10.1186/s13015-018-0133-4
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Coordinate systems for supergenomes

Abstract: BackgroundGenome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting comparative, evolutionary analysis is also growing. In particular, efficient tools to visualize-omics data simultaneously for multiple species are sorely lacking. A first and crucial step in this direction is the construction of a common coordinate system. Since genomes not only differ by rearrangeme… Show more

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Cited by 12 publications
(11 citation statements)
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“…All computations were performed on a 2.5GHz quad-core Intel Core i7 processor (Turbo Boost up to 3.7GHz) with 6MB shared L3 cache and 16GB of 1600MHz DDR3L onboard memory. Test data sets are taken from [4] and from the Stanford Large Network Dataset Collection [21]. The table lists their number N of vertices, M of edges and S of superbubbles…”
Section: Theorymentioning
confidence: 99%
See 1 more Smart Citation
“…All computations were performed on a 2.5GHz quad-core Intel Core i7 processor (Turbo Boost up to 3.7GHz) with 6MB shared L3 cache and 16GB of 1600MHz DDR3L onboard memory. Test data sets are taken from [4] and from the Stanford Large Network Dataset Collection [21]. The table lists their number N of vertices, M of edges and S of superbubbles…”
Section: Theorymentioning
confidence: 99%
“…[3]. Superbubbles also appear naturally in the multigraphs in the context of supergenome coordinatization [4], i.e., the problem of finding good common coordinate systems for multiple genomes.…”
Section: Introductionmentioning
confidence: 99%
“…This creates artefacts, because the initial alignment step by construction cannot distinguish between the individual copies of a family of loci that is subject to concerted evolution. We refer to [ 23 , 52 ] for a more extensive discussion of this issue. For mammals, we used the MultiZ alignment of 19 mammalian genomes with humans [ 53 ] and for nematodes, and the MultiZ alignment of 25 nematode genomes with Caenorhabditis elegans [ 54 ], downloadable through the University of California Santa Cruz (UCSC) Genome Browser.…”
Section: Methodsmentioning
confidence: 99%
“…All computations were performed on a 2.5-GHz quad-core Intel Core i7 processor (Turbo Boost up to 3.7 GHz) with 6-MB shared L3 cache and 16 GB of 1600-MHz DDR3L onboard memory. Test datasets were taken from [11] and from the Stanford Large Network Dataset Collection [12]. For each test graph, we list the number of vertices N, the numbers of edges M, and the number S of superbubbles.…”
mentioning
confidence: 99%