GPRED-GC : A Gene PREDiction model accounting for 5 - 3 GC gradient

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journal

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Author(s)

  • Prapaporn Techa-Angkoon
  • Kevin L. Childs
  • Yanni Sun

Related Research Unit(s)

Detail(s)

Original languageEnglish
Article number482
Journal / PublicationBMC Bioinformatics
Volume20
Issue numberSuppl 15
Online published24 Dec 2019
Publication statusPublished - 2019

Conference

Title14th International Symposium on Bioinformatics Research and Applications (ISBRA’18)
PlaceChina
CityBeijing
Period8 - 11 June 2018

Abstract

Background: Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tools and they have been widely used for gene annotation for various species. However, existing tools are not optimized for identifying genes with highly variable GC content. In addition, some genes in grass genomes exhibit a sharp 5 - 3 decreasing GC content gradient, which is not carefully modeled by available gene prediction tools. Thus, there is still room to improve the sensitivity and accuracy for predicting genes with GC gradients. 
Results: In this work, we designed and implemented a new hidden Markov model (HMM)-based ab initio gene prediction tool, which is optimized for finding genes with highly variable GC contents, such as the genes with negative GC gradients in grass genomes. We tested the tool on three datasets from Arabidopsis thaliana and Oryza sativa. The results showed that our tool can identify genes missed by existing tools due to the highly variable GC contents. 
Conclusions: GPRED-GC can effectively predict genes with highly variable GC contents without manual intervention. It provides a useful complementary tool to existing ones such as Augustus for more sensitive gene discovery. The source code is freely available at https://sourceforge.net/projects/gpred-gc/.

Research Area(s)

  • GC contents, Gene finding, Grass genomes, Hidden Markov model, Plant genome gene prediction

Citation Format(s)

GPRED-GC : A Gene PREDiction model accounting for 5 - 3 GC gradient. / Techa-Angkoon, Prapaporn; Childs, Kevin L.; Sun, Yanni.

In: BMC Bioinformatics, Vol. 20, No. Suppl 15, 482, 2019.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journal