Searching journal content for articles similar to Elhai et al. 18 (9): 1484.

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  1. Method: Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
    • John Beaulaurier,
    • Elaine Luo,
    • John M. Eppley,
    • Paul Den Uyl,
    • Xiaoguang Dai,
    • Andrew Burger,
    • Daniel J. Turner,
    • Matthew Pendelton,
    • Sissel Juul,
    • Eoghan Harrington,
    • and Edward F. DeLong
    Genome Res. March 2020 30: 437-446; Published in Advance February 19, 2020, doi:10.1101/gr.251686.119
    ...in several concatemers (Fig. 6). A similar arrangement of genes, repeats, and gene contents is known to occur in small mobile elements that can “hijack” helper-phage packaging machinery, called phage-inducible chromosomal islands (PICIs) (Penades and Christie 2015). In particular, the integrases and DNA...
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  2. Method: Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
    • Alexandre Lomsadze,
    • Karl Gemayel,
    • Shiyuyun Tang,
    • and Mark Borodovsky
    Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117
    ...containing programmed frameshifts (such as the prfB gene encoding a translation initiation factor [Craigen and Caskey 1986], or genes regulating some mobile elements [Sharma et al. 2011]). Furthermore, pseudogenes, especially expressed pseudogenes, could mislead gene-finding tools into generating predictions...
  3. Method: metaSPAdes: a new versatile metagenomic assembler
    • Sergey Nurk,
    • Dmitry Meleshko,
    • Anton Korobeynikov,
    • and Pavel A. Pevzner
    Genome Res. May 2017 27: 824-834; Published in Advance March 15, 2017, doi:10.1101/gr.213959.116
    ...for the repeat resolution approach in metaSPAdes described below. Analyzing filigree edges in the assembly graph In addition to single-nucleotide variants and small indels, strain variation is oftenmanifested as highly diverged regions, insertions of mobile elements, rearrangements, large deletions, parallel...
  4. ARTICLE: Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography
    • Philippe Normand,
    • Pascal Lapierre,
    • Louis S. Tisa,
    • Johann Peter Gogarten,
    • Nicole Alloisio,
    • Emilie Bagnarol,
    • Carla A. Bassi,
    • Alison M. Berry,
    • Derek M. Bickhart,
    • Nathalie Choisne,
    • Arnaud Couloux,
    • Benoit Cournoyer,
    • Stephane Cruveiller,
    • Vincent Daubin,
    • Nadia Demange,
    • Maria Pilar Francino,
    • Eugene Goltsman,
    • Ying Huang,
    • Olga R. Kopp,
    • Laurent Labarre,
    • Alla Lapidus,
    • Celine Lavire,
    • Joelle Marechal,
    • Michele Martinez,
    • Juliana E. Mastronunzio,
    • Beth C. Mullin,
    • James Niemann,
    • Pierre Pujic,
    • Tania Rawnsley,
    • Zoe Rouy,
    • Chantal Schenowitz,
    • Anita Sellstedt,
    • Fernando Tavares,
    • Jeffrey P. Tomkins,
    • David Vallenet,
    • Claudio Valverde,
    • Luis G. Wall,
    • Ying Wang,
    • Claudine Medigue,
    • and David R. Benson
    Genome Res. January 2007 17: 7-15; Published in Advance December 6, 2006, doi:10.1101/gr.5798407
    ...Frankia ( Fig. 1 ; Clawson et al. 2004 ). Genome characteristics The s from ACN and CcI3 have been finished, and that from EAN has been rendered in a single scaffold with some gaps corresponding to regions that have proven difficult to resolve due to sequence repeats and high GC content ( Table 2...
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