Searching journal content for articles similar to Ter-Hovhannisyan et al. 18 (12): 1979.

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  1. 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
    ...in the subsequent steps of the algorithm when it makes iterative training and prediction of the CDSs in genomic regions between the HC genes.We showed that the predicted HC genes had much higher Pr than the initial set of gene candidates (Table 1; Supplemental Fig. S7). The number of HC gene predictions made...
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  2. Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
    • Sira Sriswasdi,
    • Masako Takashima,
    • Ri-ichiroh Manabe,
    • Moriya Ohkuma,
    • Takashi Sugita,
    • and Wataru Iwasaki
    Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
    ...within a single clade of a fungal genus, Trichosporon . Comparative genomic analyses revealed that redundant genes are experiencing decelerations, not accelerations, of evolutionary rates. We identified a relationship between gene conversion and decelerated evolution suggesting that gene conversion may...
  3. 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
    ...Mark, and AUGUSTUS predictions. Although MAKER2 can provide training sets for SNAP and AUGUSTUS, it does not train the ab initio models automatically. Also, the self-training of GeneMark.hmm models (Lomsadze et al. 2005) has to be performed outside of MAKER2. FINDER follows an approach similar to BRAKER3. It uses...
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  4. 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
    ...(Table 2, below). Although “ annotation” is often treated as an omnibus term that includes both the prediction of the genomic positions of genes and constituent isoforms and the assigning of gene symbols and functions, we focus on the first of these two components. Our goals are to determine (1) which...
  5. 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
    ...with tetranucleotide frequencies, coverage, and GC content, we assigned the eukaryotic scaffolds into four bins. BLASTing gene predictions against UniProt identified three of the bins as likely fungi and a fourth as a likely metazoan. Gene prediction was redone on the new fungal bins with GeneMark-ES in self-training...
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