Searching journal content for articles similar to van Baren and Brent 16 (5): 678.

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  1. Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
    ....48 million assemblies, of which 43,120 are eukaryotes, 2.20 million are bacteria, 24,050 are archaea, and 192,600 are viruses.Genome annotation—identifying genes and other biological features—is essential to understanding the biology of these s (Stein 2001). Annotating eukaryotic s presents particular...
  2. 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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  3. Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
    • Ying Zhou,
    • Li Song,
    • and Heng Li
    Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
    ...for those nonclassical coding genes and pseudogenes. Through a series of genetic analyses, we validated Immuannot and identified numerous new genetic patterns. As long-read data become more and more popular, our tool will improve the genetic research in HLA and KIR regions.ResultsMethod overview...
  4. Method: Gene prediction in the immunoglobulin loci
    • Vikram Sirupurapu,
    • Yana Safonova,
    • and Pavel A. Pevzner
    Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
    ...as the percent identity between its v-fragment and the closest predicted gene (predicted genes could either be canonical genes from reference species or be candidate genes detected by IterativeIGDetective). A vertex is annotated if its conservation is at least PIannotation (default value = 90%). For annotating...
  5. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ..., with a special focus on de novo gene birth.View this table: In this window In a new window Table 1. Studies investigating the origin of ORFans in bacteriaORFans as artifactsOur discussion of bacterial ORFans focuses only on protein-coding annotated genes, noting that not all annotated genes are functional...
  6. Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
    • Samuel T. Horsfield,
    • Gerry Tonkin-Hill,
    • Nicholas J. Croucher,
    • and John A. Lees
    Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
    ...and causal gene annotations generated by ggCaller are available in Supplemental Figure 9.ggCaller performance scales with population variationExisting pan analysis workflows rely on iterative and usually redundant annotation of genes within independent s. In contrast, ggCaller predicts and annotates genes...
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  7. Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
    • Bertille Montibus,
    • James A. Cain,
    • Rocio T. Martinez-Nunez,
    • and Rebecca J. Oakey
    Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
    ...decided to use the GENCODE consortium genomic annotation. We used the “comprehensive” set which includes the highest number of transcripts associated with protein-coding genes, pseudogenes, long noncoding RNAs and small noncoding RNAs genes (Frankish et al. 2019). Transcripts with “to be experimentally...
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  8. Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
    • Elise Parey,
    • Alexandra Louis,
    • Jérôme Montfort,
    • Yann Guiguen,
    • Hugues Roest Crollius,
    • and Camille Berthelot
    Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
    ..., possibly driven by distinct and underappreciated factors.The comparative atlas enhances teleost gene and annotationsFinally, we investigated how the comparative atlas may improve crucial resources for fish evolutionary, ecological, and functional genomics. The Zebrafish Information Network (ZFIN) provides...
  9. 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
    ...and COG annotation (Table 2). Also, GeneMarkS-2 made the least numbers of false positive predictions in simulated noncoding sequences (Table 3B).The array of atypical models employed in GeneMarkS-2 improved the prediction of horizontally transferred (atypical) genes. In our observations, the deviation...
  10. Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
    • Étienne Fafard-Couture,
    • Pierre-Étienne Jacques,
    • and Michelle S. Scott
    Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
    ...In a new window Figure 4. Box sequence conservation, snoRNA stability, and host gene expression level govern the snoRNA expression status. (A) Distribution of the predictive rank of each input feature across all selected models and iterations. (B) Frequency logos of the observed C (top panel) and D (bottom...
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