Browsing by Subject "ASSEMBLIES"

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  • Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Simkova, Hana; Stankova, Helena; Vrana, Jan; Chan, Saki; Munoz-Amatriain, Maria; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Dolezel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin (2017)
    Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
  • Salmela, Leena; Mukherjee, Kingshuk; Puglisi, Simon J.; Muggli, Martin D.; Boucher, Christina (2020)
    Motivation: Optical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes. The challenge faced in error correction is in determining pairs of Rmaps that originate from the same region of the same genome. Results: We create an efficient method for determining pairs of Rmaps that contain significant overlaps between them. Our method relies on the novel and nontrivial adaption and application of spaced seeds in the context of optical mapping, which allows for spurious and deleted cut sites to be accounted for. We apply our method to detecting and correcting these errors. The resulting error correction method, referred to as Elmeri, improves upon the results of state-of-the-art correction methods but in a fraction of the time. More specifically, cOMet required 9.9 CPU days to error correct Rmap data generated from the human genome, whereas Elmeri required less than 15 CPU hours and improved the quality of the Rmaps by more than four times compared to cOMet.
  • Baddam, Vikram; Valinen, Lauri; Tenhu, Heikki (2021)
    Poly [(vinylbenzyl) trimethylammonium chloride] (PVBTMAC) has been used as a stabilizer in the polymerization-induced self-assembly polymerizations of diacetone acrylamide (DAAM). A whole spectrum of particle morphologies was obtained simply by adjusting the ionic strength of the reaction mixtures; no dilution of the cationic charges with noncharged comonomers or with noncharged polymers was needed. In addition to the ionic strength, the effects of solid content and the length of the PDAAM block on the morphologies of the particles were studied in detail. The experiments are a continuation to previous studies on solution properties of PVBTMAC. It has been shown earlier that the solubility of the polycation may be tuned with counterions. Hydrophobic triflate ions induce an upper critical solution temperature behavior. In the present case, the chains bound to hydrophobic cores of the particles show either a one-step phase separation in aqueous triflate solutions or under certain conditions, a two-step transition. The step-wise transition is typical for responsive polymers with limited mobility.