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

BMC Genomics
Franziska Zickmann, Bernhard Y Renard

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.

References

Oct 28, 1998·Bioinformatics·K Murakami, T Takagi
Feb 12, 2002·Bioinformatics·Vladimir PavlovićSimon Kasif
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Jul 2, 2003·Bioinformatics·Sohrab P ShahB F Francis Ouellette
Jan 7, 2004·Genome Research·Jonathan E AllenSteven L Salzberg
May 18, 2004·BMC Bioinformatics·Ian Korf
Aug 4, 2005·Bioinformatics·Jonathan E Allen, Steven L Salzberg
Jul 5, 2006·BMC Bioinformatics·Chaochun Wei, Michael R Brent
Nov 4, 2006·Journal of Proteome Research·Alon SavidorW Hayes McDonald
Jan 24, 2007·Bioinformatics·Arthur L DelcherSteven L Salzberg
Jan 24, 2007·Genome Biology·Christine G ElsikGeorge M Weinstock
Jan 15, 2011·BMC Bioinformatics·Non G Yok, Gail L Rosen
Oct 15, 2013·Bioinformatics·Franziska ZickmannBernhard Y Renard

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Citations

Feb 20, 2016·Nucleic Acids Research·Jens KeilwagenFrank Hartung
Jun 15, 2015·Bioinformatics·Franziska Zickmann, Bernhard Y Renard
Dec 10, 2016·Nucleic Acids Research·Ankita SinghB Jayaram
Jul 5, 2016·Expert Review of Proteomics·Thilo MuthLennart Martens
Jan 24, 2021·Briefings in Bioinformatics·Dropen ShekaPaul M K Gordon

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Datasets Mentioned

BETA
SRR546811
SRR1654792

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

IPred
JIGSAW
GLIMMER3
Cufflinks
EVidenceModeler
GIIRA
GLEAN
Numpy
Cuffmerge
Cuffcompare

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