Searching journal content for articles similar to Parra et al. 13 (1): 108.

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  1. 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
    ...@ucsd.eduAbstractThe V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin (IG) loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) are critical for studies of the adaptive...
  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
    ...experiments, and N-terminal protein sequencing. We observed that GeneMarkS-2 performed better on average in all accuracy measures when compared with the current state-of-the-art gene prediction tools. Furthermore, the screening of ∼5000 representative prokaryotic s made by GeneMarkS-2 predicted frequent...
  3. Methods: Conrad: Gene prediction using conditional random fields
    • David DeCaprio,
    • Jade P. Vinson,
    • Matthew D. Pearson,
    • Philip Montgomery,
    • Matthew Doherty,
    • and James E. Galagan
    Genome Res. September 2007 17: 1389-1398; Published in Advance August 9, 2007, doi:10.1101/gr.6558107
    ...Conrad: Gene prediction using conditional random fields David DeCaprio 1 , 3 , Jade P. Vinson 1 , 2 , Matthew D. Pearson 1 , Philip Montgomery 1 , Matthew Doherty 1 , and James E. Galagan 1 1 The Broad Institute...
    OPEN ACCESS ARTICLE
  4. RESOURCE: Iterative gene prediction and pseudogene removal improves genome annotation
    • Marijke J. van Baren and
    • Michael R. Brent
    Genome Res. May 2006 16: 678-685; doi:10.1101/gr.4766206
    ...Iterative gene prediction and pseudogene removal improves genome annotation PPFINDER Marijke J. van Baren and Michael R. Brent 1 Laboratory for Computational Genomics, Department of Computer Science Washington University, Saint Louis, Missouri 63130, USA...
    OPEN ACCESS ARTICLE
  5. Methods: Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    • Vardges Ter-Hovhannisyan,
    • Alexandre Lomsadze,
    • Yury O. Chernoff,
    • and Mark Borodovsky
    Genome Res. December 2008 18: 1979-1990; Published in Advance August 29, 2008, doi:10.1101/gr.081612.108
    ...Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Vardges Ter-Hovhannisyan 1 , 4 , Alexandre Lomsadze 2 , 4 , Yury O. Chernoff 1 , and Mark Borodovsky 2 , 3 , 5 1 School of Biology...
  6. Methods: Computational Gene Prediction Using Multiple Sources of Evidence
    • Jonathan E. Allen,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. January 2004 14: 142-148; doi:10.1101/gr.1562804
    ...Computational Gene Prediction Using Multiple Sources of Evidence Jonathan E. Allen 1 , 2 , 3 , Mihaela Pertea 1 , and Steven L. Salzberg 1 , 2 1 The Institute for Genomic Research, Rockville, Maryland 20850, USA 2 Department...
  7. METHODS: An Assessment of Gene Prediction Accuracy in Large DNA Sequences
    • Roderic Guigó,
    • Pankaj Agarwal,
    • Josep F. Abril,
    • Moisés Burset,
    • and James W. Fickett
    Genome Res. October 1, 2000 10: 1631-1642; doi:10.1101/gr.122800
    ...An Assessment of Gene Prediction Accuracy in Large DNA Sequences Roderic Guigó 1 , 3 , Pankaj Agarwal 2 , Josep F. Abril 1 , Moisés Burset 1 , and James W. Fickett 2 1Grup de Recerca en Informática Mèdica, Institut Municipal...
  8. Methods: Gene prediction and verification in a compact genome with numerous small introns
    • Aaron E. Tenney,
    • Randall H. Brown,
    • Charles Vaske,
    • Jennifer K. Lodge,
    • Tamara L. Doering,
    • and Michael R. Brent
    Genome Res. November 2004 14: 2330-2335; Published in Advance October 12, 2004, doi:10.1101/gr.2816704
    ...Gene prediction and verification in a compact genome with numerous small introns Aaron E. Tenney 1 , Randall H. Brown 1 , Charles Vaske 1 , 4 , Jennifer K. Lodge 2 , Tamara L. Doering 3 , and Michael R. Brent 1 , 5...
  9. Methods: Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing
    • Jia Qian Wu,
    • David Shteynberg,
    • Manimozhiyan Arumugam,
    • Richard A. Gibbs,
    • and Michael R. Brent
    Genome Res. April 2004 14: 665-671; doi:10.1101/gr.1959604
    ...Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing Jia Qian Wu 1 , David Shteynberg 2 , Manimozhiyan Arumugam 2 , Richard A. Gibbs 1 , and Michael R. Brent 2 , 3 1 Human Genome Sequencing...
  10. Methods: Gene Prediction by Spectral Rotation Measure: A New Method for Identifying Protein-Coding Regions
    • Daniel Kotlar and
    • Yizhar Lavner
    Genome Res. August 2003 13: 1930-1937; Published in Advance July 17, 2003, doi:10.1101/gr.1261703
    ...Gene Prediction by Spectral Rotation Measure: A New Method for Identifying Protein-Coding Regions Daniel Kotlar and Yizhar Lavner 1 Department of Computer Science, Tel-Hai Academic College, Upper Galilee 12210, Israel Abstract A new measure...
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