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Resource: Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
- LaDeana W. Hillier,
- Valerie Reinke,
- Philip Green,
- Martin Hirst,
- Marco A. Marra,
- and Robert H. Waterston
Genome Res. April 2009 19: 657-666; Published in Advance January 30, 2009, doi:10.1101/gr.088112.108
...-generation sequencing we have been able to sample RNA far more deeply than has been previously possible, and as a result provide evidence for a large set of protein-coding genes and exons in C. elegans that had no previous experimental support. The results incorporate predictions from WormBase, Twinscan, and Genefinder...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...conserved across species, making their identification by either computational or experimental means more difficult. Improvements in gene prediction programs may help tease out these signals. Twinscan ( Korf et al. 2001 ), an HMM-based program derived from GenScan ( Burge and Karlin 1997 ) that can use...
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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
...information that is invaluable for annotation. In fact, a project aimed at obtaining full ORF clones of all Caenorhabditis elegans genes using the predictions of the program Gene Finder (P. Green, unpubl.) has produced good results ( Reboul et al. 2003 ), and TWINSCAN predictions are now being used to fill...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...Abstract To learn how well ungapped sequence comparisons of multiple species can predict cis -regulatory elements in Caenorhabditis elegans , we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied...
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Resource: RNA-seq analysis of the C. briggsae transcriptome
- Bora Uyar,
- Jeffrey S.C. Chu,
- Ismael A. Vergara,
- Shu Yi Chua,
- Martin R. Jones,
- Tammy Wong,
- David L. Baillie,
- and Nansheng Chen
Genome Res. August 2012 22: 1567-1580; Published in Advance July 6, 2012, doi:10.1101/gr.134601.111
...(Vandenberghe et al. 2001). In C. elegans, operons were first observed by Blumenthal and colleagues (Spieth et al. 1993). Operons in nematodes have been known to be closely Figure 3. RNA-seq revisions of C. briggsae gene models. (A) An intron is confirmed if the predicted intron in the hybrid gene model...
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PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
- Michael R. Brent
Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
..., or even fragments of several genes from the same family. Flicek et al. ( 2003 ) reported that TWINSCAN was able to predict 14% of known ORFs in the human correctly. Although SGP2 was tested only on chromosome 22, which is unusually gene dense compared with the whole , the accuracies of the two systems...
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LETTER: Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans
- Quinn M. Mitrovich,
- Brian B. Tuch,
- Christine Guthrie,
- and Alexander D. Johnson
Genome Res. April 2007 17: 492-502; Published in Advance March 9, 2007, doi:10.1101/gr.6111907
...inconsistent with phylogenetic data—the putative splice sites are not conserved in closely related species, and splicing of the putative introns would disrupt conserved coding sequences. Our algorithm does not predict a discrete boundary between genes that do and genes that do not contain introns ( Fig. 3...

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