Dataset Information

Method of predicting splice sites based on signal interactions.

ABSTRACT:

Background

Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan.

Results

According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments.

Conclusion

Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site.

Reviewers

This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

SUBMITTER: Churbanov A

PROVIDER: S-EPMC1526722 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature

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Publications

Method of predicting splice sites based on signal interactions.

Churbanov Alexander A Rogozin Igor B IB Deogun Jitender S JS Ali Hesham H

Biology direct 20060403

<h4>Background</h4>Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detecti ...[more]

PMID: 16584568

Similar Datasets

Project description:BackgroundSplice sites prediction has been a long-standing problem in bioinformatics. Although many computational approaches developed for splice site prediction have achieved satisfactory accuracy, further improvement in predictive accuracy is significant, for it is contributing to predict gene structure more accurately. Determining a proper window size before prediction is necessary. Overly long window size may introduce some irrelevant features, which would reduce predictive accuracy, while the use of short window size with maximum information may performs better in terms of predictive accuracy and time cost. Furthermore, the number of false splice sites following the GT-AG rule far exceeds that of true splice sites, accurate and rapid prediction of splice sites using imbalanced large samples has always been a challenge. Therefore, based on the short window size and imbalanced large samples, we developed a new computational method named chi-square decision table (χ2-DT) for donor splice site prediction.ResultsUsing a short window size of 11 bp, χ2-DT extracts the improved positional features and compositional features based on chi-square test, then introduces features one by one based on information gain, and constructs a balanced decision table aimed at implementing imbalanced pattern classification. With a 2000:271,132 (true sites:false sites) training set, χ2-DT achieves the highest independent test accuracy (93.34%) when compared with three classifiers (random forest, artificial neural network, and relaxed variable kernel density estimator) and takes a short computation time (89 s). χ2-DT also exhibits good independent test accuracy (92.40%), when validated with BG-570 mutated sequences with frameshift errors (nucleotide insertions and deletions). Moreover, χ2-DT is compared with the long-window size-based methods and the short-window size-based methods, and is found to perform better than all of them in terms of predictive accuracy.ConclusionsBased on short window size and imbalanced large samples, the proposed method not only achieves higher predictive accuracy than some existing methods, but also has high computational speed and good robustness against nucleotide insertions and deletions.ReviewersThis article was reviewed by Ryan McGinty, Ph.D. and Dirk Walther.

Dataset Information

Method of predicting splice sites based on signal interactions.

Background

Results

Conclusion

Reviewers

Publications

Method of predicting splice sites based on signal interactions.

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