Searching journal content for articles similar to Stormo 10 (4): 394.

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  1. Method: Genome-reconstruction for eukaryotes from complex natural microbial communities
    • Patrick T. West,
    • Alexander J. Probst,
    • Igor V. Grigoriev,
    • Brian C. Thomas,
    • and Jillian F. Banfield
    Genome Res. April 2018 28: 569-580; Published in Advance March 1, 2018, doi:10.1101/gr.228429.117
    ..., California 94720, USA ↵6 Present address: Group for Aquatic Microbial Ecology, Biofilm Center, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany Corresponding author: Jbanfield@berkeley.eduAbstractMicrobial eukaryotes are integral components of natural microbial communities...
  2. Resource: mGene: Accurate SVM-based gene finding with an application to nematode genomes
    • Gabriele Schweikert,
    • Alexander Zien,
    • Georg Zeller,
    • Jonas Behr,
    • Christoph Dieterich,
    • Cheng Soon Ong,
    • Petra Philips,
    • Fabio De Bona,
    • Lisa Hartmann,
    • Anja Bohlen,
    • Nina Krüger,
    • Sören Sonnenburg,
    • and Gunnar Rätsch
    Genome Res. November 2009 19: 2133-2143; Published in Advance June 29, 2009, doi:10.1101/gr.090597.108
    ...mGene: Accurate SVM-based gene finding with an application to nematode genomes Gabriele Schweikert 1 , 2 , 3 , Alexander Zien 1 , 4 , 5 , Georg Zeller 1 , 3 , 5 , Jonas Behr 1 , Christoph Dieterich 3 , 6 , Cheng Soon Ong 1...
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  3. METHODS: Genie—Gene Finding in Drosophila melanogaster
    • Martin G. Reese,
    • David Kulp,
    • Hari Tammana,
    • and David Haussler
    Genome Res. April 1, 2000 10: 529-538; doi:10.1101/gr.10.4.529
    ...Genie —Gene Finding in Drosophila melanogaster Martin G. Reese 1 , 2 , 4 , David Kulp 2 , Hari Tammana 2 , and David Haussler 2 , 3 1Berkeley Drosophila Genome Project, Department of Molecular and Cell Biology, University...
  4. LETTER: Evaluation of Gene-Finding Programs on Mammalian Sequences
    • Sanja Rogic,
    • Alan K. Mackworth,
    • and Francis B.F. Ouellette
    Genome Res. May 1, 2001 11: 817-832; doi:10.1101/gr.147901
    ...methods for gene-finding. Gene Structure The genes of most eukaryotic organisms are neither continuous nor contiguous. They are separated by long stretches of intergenic DNA and their coding sequences are interrupted by noncoding introns. Coding sequences occupy just a small fraction of a typical higher...
  5. METHODS: Ab initio Gene Finding in Drosophila Genomic DNA
    • Asaf A. Salamov and
    • Victor V. Solovyev
    Genome Res. April 1, 2000 10: 516-522; doi:10.1101/gr.10.4.516
    ...Ab initio Gene Finding in Drosophila Genomic DNA Asaf A. Salamov and Victor V. Solovyev 1 The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Abstract Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained...
  6. Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
    • Ming Yan,
    • Thea O. Andersen,
    • Phillip B. Pope,
    • and Zhongtang Yu
    Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
    ...abundance and low fungal DNA yield from rumen fluid samples because rumen fungi strongly adhere to digesta particles. We assessed the completeness of the identified eukaryotic bins based on the presence of lineage-resolved single-copy marker genes, finding that most bins were largely incomplete, consistent...
  7. Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
    • Lars Gabriel,
    • Tomáš Brůna,
    • Katharina J. Hoff,
    • Matthis Ebel,
    • Alexandre Lomsadze,
    • Mark Borodovsky,
    • and Mario Stanke
    Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
    .... We have shown that BRAKER3 consistently outperformed the other gene finding tools.MethodsBRAKER3BRAKER3 is the latest annotation pipeline that continues the BRAKER family. It requires three types of inputs: the sequence to annotate, a list of short-read RNA-seq data sets, and a protein database file...
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  8. Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
    • Tomáš Brůna,
    • Alexandre Lomsadze,
    • and Mark Borodovsky
    Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
    ...(including all alternative CDSs)Assessment of the gene-prediction accuracyThe accuracy of previously developed gene-finding tools shows a consistent decline with the increase in the length of eukaryotic . This pattern is because of the increasing difficulty of accurately finding protein-coding sequences...
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  9. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    ...kb mitochondrial , for which we obtained a complete and circularized sequence, whereas contigs 19–29 contain only 45S rDNA arrays. We found an enrichment of TTAGGG telomere repeats, typical of many eukaryotes, including true truffles (Martin et al. 2010), toward both ends of all 17 majors nuclear...
  10. Resource: Building better genome annotations across the tree of life
    • Adam H. Freedman and
    • Timothy B. Sackton
    Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
    ...://www.ncbi.nlm.nih.gov/datasets//). NCBI has annotated <50% of all of its hosted eukaryotic reference s, amounting to <20% of all eukaryotic s (https://www.ncbi.nlm.nih.gov/datasets//). Given the current rate of annotation by NCBI, it is hard to imagine that it will keep pace with the rate at which new s are assembled. Additional...
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