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GeneBuilder: interactive in silico prediction of gene structure
L Milanesi1, D D'Angelo, I B Rogozin
1Istituto di Tecnologie Biomediche Avanzate CNR, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy. milanesi@itba.mi.cnr.it
Bioinformatics (Oxford, England)
|September 17, 1999
Summary
GeneBuilder predicts eukaryotic gene structures by combining functional signals and statistical properties. This system achieves high accuracy in gene structure prediction, even with low sequence homology.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Accurate gene structure prediction is crucial for large-scale genome sequencing projects.
- Eukaryotic gene complexity arises from exon-intron structures and regulatory nucleotide domains.
- Analyzing full gene structures requires integrating functional signals, coding potential, homology, and repeat elements.
Purpose of the Study:
- To develop a computational system for predicting eukaryotic gene structures.
- To improve the accuracy of gene structure prediction by integrating diverse biological data.
- To provide a tool for analyzing gene organization in newly sequenced genomes.
Main Methods:
- Developed the GeneBuilder system integrating functional signal prediction and coding region analysis.
- Employed dynamic programming for generating potential gene structure models.
- Incorporated similarity searches against protein and EST databases.
- Allowed parameter customization for gene structure prediction and refinement.
Main Results:
- GeneBuilder demonstrated high performance with 0.89 sensitivity and 0.91 specificity at the nucleotide level.
- Achieved a total correlation coefficient of 0.88 on a standard test set.
- Showed improved prediction accuracy by selecting appropriate exon homology levels.
- Successfully predicted gene structures even in cases of low sequence homology.
Conclusions:
- GeneBuilder is an effective system for predicting eukaryotic gene structures.
- The system's accuracy is robust, performing well even with limited sequence similarity.
- GeneBuilder provides a valuable tool for genomic analysis and research.