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RESOURCE: Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
- Chaochun Wei,
- Philippe Lamesch,
- Manimozhiyan Arumugam,
- Jennifer Rosenberg,
- Ping Hu,
- Marc Vidal,
- and Michael R. Brent
Genome Res. April 2005 15: 577-582; doi:10.1101/gr.3329005
...: 554 -571. ↵ Wu, J.Q., Shteynberg, D., Arumugam, M., Gibbs, R.A., and Brent, M.R. 2004 . Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res. 14 : 665 -671. Web site references ↵ http...
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Methods: Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat
- Colin Dewey,
- Jia Qian Wu,
- Simon Cawley,
- Marina Alexandersson,
- Richard Gibbs,
- and Lior Pachter
Genome Res. April 2004 14: 661-664; doi:10.1101/gr.1939804
...human genes and their simultaneously predicted rat orthologs. The gels contain the RT-PCR sequenced products from human ( A ) and rat ( B ). Each column in the gel contains the sequenced product for one intron tested, with the same columns in the human and rat gels containing products from orthologous...
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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
.... ↵ Wu, J.Q., Shteynberg, D., Arumugam, M., Gibbs, R.A., and Brent, M.R. 2004 . Identification of rat genes by TWINSCAN gene prediction, RT–PCR, and direct sequencing. Genome Res. 14 : 665 -671. WEB SITE REFERENCES ↵ http://www.ncbi.nlm.nih.gov/Traces/ ; NCBI Trace Archive. http://genes...
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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
...data suggest some genes or exons are missing altogether from the current WormBase predictions ( Merrihew et al. 2008 ). To remedy this situation, one of us (P. Green) has for several years undertaken a directed approach utilizing RT-PCR and RACE to test the remaining unconfirmed splice junctions...
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Methods: A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
- Aaron E. Tenney,
- Jia Qian Wu,
- Laura Langton,
- Paul Klueh,
- Ralph Quatrano,
- and Michael R. Brent
Genome Res. February 2007 17: 212-218; Published in Advance January 8, 2007, doi:10.1101/gr.5661407
...by TWINSCAN gene prediction, RT-PCR, and direct sequencing . Genome Res. 14 : 665 – 671 . A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices Aaron E. Tenney 1 , 4 , Jia Qian Wu 2 , 4 , Laura Langton 1 , Paul...
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Methods: Targeted discovery of novel human exons by comparative genomics
- Adam Siepel,
- Mark Diekhans,
- Broňa Brejová,
- Laura Langton,
- Michael Stevens,
- Charles L.G. Comstock,
- Colleen Davis,
- Brent Ewing,
- Shelly Oommen,
- Christopher Lau,
- Hung-Chun Yu,
- Jianfeng Li,
- Bruce A. Roe,
- Phil Green,
- Daniela S. Gerhard,
- Gary Temple,
- David Haussler,
- and Michael R. Brent
Genome Res. December 2007 17: 1763-1773; Published in Advance November 7, 2007, doi:10.1101/gr.7128207
...) project, to identify human genes not yet in the gene catalogs. Our approach was to produce gene predictions by algorithms that rely on comparative sequence data but do not require direct cDNA evidence, then to test predicted novel genes by RT–PCR. We have identified 734 novel gene fragments (NGFs...
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RESOURCE: Begin at the beginning: Predicting genes with 5′ UTRs
- Randall H. Brown,
- Samuel S. Gross,
- and Michael R. Brent
Genome Res. May 2005 15: 742-747; doi:10.1101/gr.3696205
...for this application. For full ORF gene verification using RT-PCR followed by direct sequencing, it is desirable to place one primer in an exonic region upstream of the start codon. If the primer anneals too close to the start codon, then the region of high-quality sequencing trace may begin after the start codon...
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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
...by sequencing of the amplicons. To amplify cDNAs, we need reasonably accurate, though not necessarily perfect, gene predictions to use for PCR primer design. The further a prediction is from a true gene structure, the greater the likelihood that PCR primers designed for it will fail. Each failure increases...
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REVIEW: Cross-Species Sequence Comparisons: A Review of Methods and Available Resources
- Kelly A. Frazer,
- Laura Elnitski,
- Deanna M. Church,
- Inna Dubchak,
- and Ross C. Hardison
Genome Res. January 1, 2003 13: 1-12; doi:10.1101/gr.222003
...), the corresponding genes are considered as being putative orthologs. The calculated orthologous relationships for ST7 human, cow, mouse, and rat gene sequences are shown in Figure 3 . For these four species, all six pairwise transcript sequence comparisons identified the ST7 gene as the reciprocal best match...

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