Searching journal content for articles similar to Wiehe et al. 11 (9): 1574.

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  1. METHODS: Comparative Gene Prediction in Human and Mouse
    • Genı́s Parra,
    • Pankaj Agarwal,
    • Josep F. Abril,
    • Thomas Wiehe,
    • James W. Fickett,
    • and Roderic Guigó
    Genome Res. January 1, 2003 13: 108-117; doi:10.1101/gr.871403
    .... The programs ROSSETA ( Batzoglou et al. 2000 ), SGP1 (from ‘syntenic gene prediction’; Wiehe et al. 2001 ), and CEM (from ‘conserved exon method’; Bafna and Huson 2000 ) are representative of this approach. All these programs start by aligning two syntenic sequences and then predict gene structures in which...
  2. METHODS: SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model
    • Marina Alexandersson,
    • Simon Cawley,
    • and Lior Pachter
    Genome Res. March 1, 2003 13: 496-502; Published in Advance February 12, 2003, doi:10.1101/gr.424203
    ...://genes.cs.wustl.edu ), SGP-1 ( Wiehe et al. 2001 ; http://www1.imim.es/datasets/humanmouse ), and SGP-2 (R. Guigó, pers. comm.). These programs differ from the homology-based gene finders such as PROCRUSTES ( Gelfand et al. 1996 ), GENOMESCAN ( Yeh et al. 2001 ), and GENEWISE2 ( Birney and Durbin 2000 ) in that rather than...
  3. Method: Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
    • Markus Brosch,
    • Gary I. Saunders,
    • Adam Frankish,
    • Mark O. Collins,
    • Lu Yu,
    • James Wright,
    • Ruth Verstraten,
    • David J. Adams,
    • Jennifer Harrow,
    • Jyoti S. Choudhary,
    • and Tim Hubbard
    Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
    ...matching with genome-wide protein-coding predictions to perform large-scale gene validation and discovery in the mouse genome for the first time. In searching an excess of 10 million spectra, we have been able to validate 32%, 17%, and 7% of all protein-coding genes, exons, and splice boundaries...
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  4. RESOURCE: BLAT—The BLAST-Like Alignment Tool
    • W. James Kent
    Genome Res. April 1, 2002 12: 656-664; Published in Advance March 20, 2002, doi:10.1101/gr.229202
    ...bias for coding region identification. J. Comput. Biol. 1 : 39 – 50 . ↵ Wiehe T. , Gebauer-Jung S. , Mitchell-Olds T. , Guigo R. ( 2001 ) SGP-1: Prediction and validation of homologous genes based on sequence alignments. Genome Res. 11 : 1574 – 1583 . ↵ Zhang Z. , Schwartz S. , Wagner L. , Miller W...
  5. ARTICLE: Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
    • Hidehiro Toh,
    • Brian L. Weiss,
    • Sarah A.H. Perkin,
    • Atsushi Yamashita,
    • Kenshiro Oshima,
    • Masahira Hattori,
    • and Serap Aksoy
    Genome Res. February 2006 16: 149-156; Published in Advance December 19, 2005, doi:10.1101/gr.4106106
    ..., and Yersinia , the size distribution of Sodalis ' CDSs indicates that its encodes a lower percentage of large protein products ( Fig. 2 ). These data suggest that the Sodalis contains a significant number of fragmented CDSs or pseudogenes. Alignment of these pseudogenes with their functional homologs validated...
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