Dataset Information

IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy.

ABSTRACT: Gene prediction is a challenging but crucial part in most genome analysis pipelines. Various methods have evolved that predict genes ab initio on reference sequences or evidence based with the help of additional information, such as RNA-Seq reads or EST libraries. However, none of these strategies is bias-free and one method alone does not necessarily provide a complete set of accurate predictions.We present IPred (Integrative gene Prediction), a method to integrate ab initio and evidence based gene identifications to complement the advantages of different prediction strategies. IPred builds on the output of gene finders and generates a new combined set of gene identifications, representing the integrated evidence of the single method predictions.We evaluate IPred in simulations and real data experiments on Escherichia Coli and human data. We show that IPred improves the prediction accuracy in comparison to single method predictions and to existing methods for prediction combination.

SUBMITTER: Zickmann F

PROVIDER: S-EPMC4345001 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy.

Zickmann Franziska F Renard Bernhard Y BY

BMC genomics 20150226

<h4>Background</h4>Gene prediction is a challenging but crucial part in most genome analysis pipelines. Various methods have evolved that predict genes ab initio on reference sequences or evidence based with the help of additional information, such as RNA-Seq reads or EST libraries. However, none of these strategies is bias-free and one method alone does not necessarily provide a complete set of accurate predictions.<h4>Results</h4>We present IPred (Integrative gene Prediction), a method to inte ...[more]

PMID: 25766582

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Project description:BACKGROUND:Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures. RESULTS:We describe novel systems for the prediction of protein domain boundaries powered by Recursive Neural Networks. The systems rely on a combination of primary sequence and evolutionary information, predictions of structural features such as secondary structure, solvent accessibility and residue contact maps, and structural templates, both annotated for domains (from the SCOP dataset) and unannotated (from the PDB). We gauge the contribution of contact maps, and PDB and SCOP templates independently and for different ranges of template quality. We find that accurately predicted contact maps are informative for the prediction of domain boundaries, while the same is not true for contact maps predicted ab initio. We also find that gap information from PDB templates is informative, but, not surprisingly, less than SCOP annotations. We test both systems trained on templates of all qualities, and systems trained only on templates of marginal similarity to the query (less than 25% sequence identity). While the first batch of systems produces near perfect predictions in the presence of fair to good templates, the second batch outperforms or match ab initio predictors down to essentially any level of template quality.We test all systems in 5-fold cross-validation on a large non-redundant set of multi-domain and single domain proteins. The final predictors are state-of-the-art, with a template-less prediction boundary recall of 50.8% (precision 38.7%) within +/- 20 residues and a single domain recall of 80.3% (precision 78.1%). The SCOP-based predictors achieve a boundary recall of 74% (precision 77.1%) again within +/- 20 residues, and classify single domain proteins as such in over 85% of cases, when we allow a mix of bad and good quality templates. If we only allow marginal templates (max 25% sequence identity to the query) the scores remain high, with boundary recall and precision of 59% and 66.3%, and 80% of all single domain proteins predicted correctly. CONCLUSION:The systems presented here may prove useful in large-scale annotation of protein domains in proteins of unknown structure. The methods are available as public web servers at the address: http://distill.ucd.ie/shandy/ and we plan on running them on a multi-genomic scale and make the results public in the near future.

Dataset Information

IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy.

Publications

IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy.

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