EGID: an ensemble algorithm for improved genomic island detection in genomic sequences

Journal Title: Bioinformation - Year 2011, Vol 7, Issue 6

Abstract

Genomicislands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID.

Authors and Affiliations

Dongsheng Che, Mohammad Hasan, Han Wang, John Fazekas, Jinling Huang, Qi Liu

Keywords

Related Articles

High temperature unfolding of Bacillus anthracis amidase-03 by molecular dynamics simulations.

The stability of amidase-03 structure (a cell wall hydrolase protein) from Bacillus anthracis was studied using classical molecular dynamics (MD) simulation. This protein (GenBank accession number: NP_844822) contains an...

Binding site prediction of galanin peptide using evolutionary trace method.

Galanin is a neuropeptide with aminoacid length ranging from 29 to 31 is widely distributed in central and peripheral nervous system. Galanin controls various psychological processes such as sensation of pain, learning,...

Structural prediction and analysis of VIH-related peptides from selected crustacean species

The tentative elucidation of the 3D-structure of vitellogenesis inhibiting hormone (VIH) peptides is conversely underprivileged by difficulties in gaining enough peptide or protein, diffracting crystals, and numerous ext...

ProPAS: standalone software to analyze protein properties

Physicochemical properties of proteins/peptides are often used to separate proteins/peptides from complex biological samples in proteomics research, which is necessary for the further proteins/peptides identification. So...

Recent trends in remote homology detection: an Indian Medley.

The development of remote homology detection methods is a challenging area in Bioinformatics. Sequence analysis-based approaches that address this problem have employed the use of profiles, templates and Hidden Markov Mo...

Download PDF file
  • EP ID EP86040
  • DOI 10.6026/97320630007311
  • Views 180
  • Downloads 0

How To Cite

Dongsheng Che, Mohammad Hasan, Han Wang, John Fazekas, Jinling Huang, Qi Liu (2011). EGID: an ensemble algorithm for improved genomic island detection in genomic sequences. Bioinformation, 7(6), 311-314. https://europub.co.uk/articles/-A-86040