GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming
Open Access
- 1 September 2002
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 12 (9), 1418-1427
- https://doi.org/10.1101/gr.149502
Abstract
We describe a method (implemented in a program, GAZE) for assembling arbitrary evidence for individual gene components (features) into predictions of complete gene structures. Our system is generic in that both the features themselves, and the model of gene structure against which potential assemblies are validated and scored, are external to the system and supplied by the user. GAZE uses a dynamic programming algorithm to obtain the highest scoring gene structure according to the model and posterior probabilities that each input feature is part of a gene. A novel pruning strategy ensures that the algorithm has a run-time effectively linear in sequence length. To demonstrate the flexibility of our system in the incorporation of additional evidence into the gene prediction process, we show how it can be used to both represent nonstandard gene structures (in the form oftrans-spliced genes in Caenorhabditis elegans), and make use of similarity information (in the form of Expressed Sequence Tag alignments), while requiring no change to the underlying software. GAZE is available athttp://www.sanger.ac.uk/Software/analysis/GAZE.Keywords
This publication has 20 references indexed in Scilit:
- Computational Inference of Homologous Gene Structures in the Human GenomeGenome Research, 2001
- An Assessment of Gene Prediction Accuracy in Large DNA SequencesGenome Research, 2000
- Genie—Gene Finding in Drosophila melanogasterGenome Research, 2000
- Ab initio Gene Finding in Drosophila Genomic DNAGenome Research, 2000
- Using Database Matches with HMMGene for Automated Gene Detection in DrosophilaGenome Research, 2000
- Prediction of complete gene structures in human genomic DNAJournal of Molecular Biology, 1997
- Constructing gene models from accurately predicted exons: an application of dynamic programmingBioinformatics, 1994
- Prediction of gene structureJournal of Molecular Biology, 1992
- A tutorial on hidden Markov models and selected applications in speech recognitionProceedings of the IEEE, 1989
- A trans-spliced leader sequence on actin mRNA in C. elegansCell, 1987