The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.
Integrating genomic homology into gene structure prediction
Abstract
Twinscan is a new gene-structure prediction system that directly extends the probability model of Genscan, allowing it to exploit homology between two related genomes. Separate probability models are used for conservation in exons, introns, splice sites, and UTRs, reflecting the differences among their patterns of evolutionary conservation. Twinscan is specifically designed for the analysis of high-throughput genomic sequences containing an unknown number of genes. In experiments on high-throughput mouse sequences, using homologous sequences from the human genome, Twinscan shows notable improvement over Genscan in exon sensitivity and specificity and dramatic improvement in exact gene sensitivity and specificity. This improvement can be attributed entirely to modeling the patterns of evolutionary conservation in genomic sequence. Contact: ikorf@cs.wustl.edu; pflicek@cs.wustl.edu; duan@cs.wustl.edu; brent@cs.wustl.edu
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Cites
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Cited by
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
AUGUSTUS: ab initio prediction of alternative transcripts
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., & Morgenstern, B. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl200 · Cited by 2,829
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
Wu, T. D., & Watanabe, C. K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti310 · Cited by 2,354
The genome of the domesticated apple (Malus × domestica Borkh.)
Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., Bhatnagar, S. K., Troggio, M., Pruss, D., et al. (2010) · Nature Genetics · doi:10.1038/ng.654 · Cited by 2,075
Gene prediction with a hidden Markov model and a new intron submodel
Stanke, M., & Waack, S. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1080 · Cited by 1,439
Metadata
- Authors
- Korf, I., Flicek, P., Duan, D., & Brent, M. R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-06-01
- Volume
- 17
- Issue
- suppl_1
- Pages
- S140-S148
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2142418779
- Cited by
- 466
- References
- 20
- FWCI
- 13.35
- Type
- journal article
- Language
- en
- Open access
- closed
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