GeneSplicer: a new computational method for splice site prediction - PubMed (original) (raw)
GeneSplicer: a new computational method for splice site prediction
M Pertea et al. Nucleic Acids Res. 2001.
Abstract
GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.
Figures
Figure 1
False positive versus false negative rates on human acceptor sites for GeneSplicer both with and without the local maximal score filter, and for NNSplice.
Figure 2
False positive versus false negative rates on human donor sites for GeneSplicer both with and without the local maximal score filter, and for NNSplice.
Similar articles
- A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.
Pertea M, Mount SM, Salzberg SL. Pertea M, et al. BMC Bioinformatics. 2007 May 21;8:159. doi: 10.1186/1471-2105-8-159. BMC Bioinformatics. 2007. PMID: 17517127 Free PMC article. - Splice site prediction with quadratic discriminant analysis using diversity measure.
Zhang L, Luo L. Zhang L, et al. Nucleic Acids Res. 2003 Nov 1;31(21):6214-20. doi: 10.1093/nar/gkg805. Nucleic Acids Res. 2003. PMID: 14576308 Free PMC article. - Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.
Pavy N, Rombauts S, Déhais P, Mathé C, Ramana DV, Leroy P, Rouzé P. Pavy N, et al. Bioinformatics. 1999 Nov;15(11):887-99. doi: 10.1093/bioinformatics/15.11.887. Bioinformatics. 1999. PMID: 10743555 - Current methods of gene prediction, their strengths and weaknesses.
Mathé C, Sagot MF, Schiex T, Rouzé P. Mathé C, et al. Nucleic Acids Res. 2002 Oct 1;30(19):4103-17. doi: 10.1093/nar/gkf543. Nucleic Acids Res. 2002. PMID: 12364589 Free PMC article. Review. - Computational modeling of gene structure in Arabidopsis thaliana.
Brendel V, Zhu W. Brendel V, et al. Plant Mol Biol. 2002 Jan;48(1-2):49-58. Plant Mol Biol. 2002. PMID: 11860212 Review.
Cited by
- Uncovering recessive alleles in rare Mendelian disorders by genome sequencing of 174 individuals with monoallelic pathogenic variants.
Schobers G, Pennings M, de Vries J, Kwint M, van Reeuwijk J, Corominas Galbany J, van Beek R, Kamping E, Timmermans R, Kamsteeg EJ, Haer-Wigman L, Cremers FPM, Roosing S, Gilissen C, Kremer H, Brunner HG, Yntema HG, Vissers LELM. Schobers G, et al. Eur J Hum Genet. 2024 Sep 27. doi: 10.1038/s41431-024-01694-9. Online ahead of print. Eur J Hum Genet. 2024. PMID: 39333430 - Splam: a deep-learning-based splice site predictor that improves spliced alignments.
Chao KH, Mao A, Salzberg SL, Pertea M. Chao KH, et al. Genome Biol. 2024 Sep 16;25(1):243. doi: 10.1186/s13059-024-03379-4. Genome Biol. 2024. PMID: 39285451 Free PMC article. - Nanopore Deep Sequencing as a Tool to Characterize and Quantify Aberrant Splicing Caused by Variants in Inherited Retinal Dystrophy Genes.
Maggi J, Feil S, Gloggnitzer J, Maggi K, Bachmann-Gagescu R, Gerth-Kahlert C, Koller S, Berger W. Maggi J, et al. Int J Mol Sci. 2024 Sep 3;25(17):9569. doi: 10.3390/ijms25179569. Int J Mol Sci. 2024. PMID: 39273516 Free PMC article. - Investigation of cryptic JAG1 splice variants as a cause of Alagille syndrome and performance evaluation of splice predictor tools.
Keefer-Jacques E, Valente N, Jacko AM, Matwijec G, Reese A, Tekriwal A, Loomes KM, Spinner NB, Gilbert MA. Keefer-Jacques E, et al. HGG Adv. 2024 Oct 10;5(4):100351. doi: 10.1016/j.xhgg.2024.100351. Epub 2024 Sep 6. HGG Adv. 2024. PMID: 39244638 Free PMC article. - An effective deep learning-based approach for splice site identification in gene expression.
Ali M, Shah D, Qazi S, Khan IA, Abrar M, Zahir S. Ali M, et al. Sci Prog. 2024 Jul-Sep;107(3):368504241266588. doi: 10.1177/00368504241266588. Sci Prog. 2024. PMID: 39051530 Free PMC article.
References
- Burge C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78–94. - PubMed
- Berget S. (1995) Exon recognition in vertebrate splicing. J. Biol. Chem., 270, 2411–2414. - PubMed
- Moore M.J., Query,C.C. and Sharp,P.A. (1993) In Gesteland,R. and Atkins,J. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 303–357.
- Salzberg S., Delcher,A., Fasman,K. and Henderson,J. (1998) A decision tree system for finding genes in DNA. J. Comput. Biol., 5, 667–680. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources