iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets

Nucleic Acids Research, vol. 50, pp. W434–W447

Abstract

The rapid accumulation of molecular data motivates development of innovative approaches to computationally characterize sequences, structures and functions of biological and chemical molecules in an efficient, accessible and accurate manner. Notwithstanding several computational tools that characterize protein or nucleic acids data, there are no one-stop computational toolkits that comprehensively characterize a wide range of biomolecules. We address this vital need by developing a holistic platform that generates features from sequence and structural data for a diverse collection of molecule types. Our freely available and easy-to-use iFeatureOmega platform generates, analyzes and visualizes 189 representations for biological sequences, structures and ligands. To the best of our knowledge, iFeatureOmega provides the largest scope when directly compared to the current solutions, in terms of the number of feature extraction and analysis approaches and coverage of different molecules. We release three versions of iFeatureOmega including a webserver, command line interface and graphical interface to satisfy needs of experienced bioinformaticians and less computer-savvy biologists and biochemists. With the assistance of iFeatureOmega, users can encode their molecular data into representations that facilitate construction of predictive models and analytical studies. We highlight benefits of iFeatureOmega based on three research applications, demonstrating how it can be used to accelerate and streamline research in bioinformatics, computational biology, and cheminformatics areas. The iFeatureOmega webserver is freely available at http://ifeatureomega.erc.monash.edu and the standalone versions can be downloaded from https://github.com/Superzchen/iFeatureOmega-GUI/ and https://github.com/Superzchen/iFeatureOmega-CLI/.

Authors 13

1. Zhen Chen

   Henan Agricultural University

   Affiliation as printed

   Center for Crop Genome Engineering, Henan Agricultural University , Zhengzhou 450046, China

   Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou 450046, China

2. Xuhan Liu Aachen Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research , Einsteinweg 55, Leiden 2333 CC, The Netherlands

3. Pei Zhao

   Chinese Academy of Agricultural Sciences · State Key Laboratory of Cotton Biology

   Affiliation as printed

   State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS) , Anyang 455000, China

4. Chen Li

   Monash University

   Affiliation as printed

   Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800, Australia

5. Yanan Wang

   Monash University

   Affiliation as printed

   Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800, Australia

6. Fuyi Li

   Monash University

   Affiliation as printed

   Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800, Australia

7. Tatsuya Akutsu

   Kyoto University · Kyoto University Institute for Chemical Research

   Affiliation as printed

   Bioinformatics Center, Institute for Chemical Research, Kyoto University , Kyoto 611-0011, Japan

8. Robin B. Gasser

   The University of Melbourne

   Affiliation as printed

   Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne , Parkville, Victoria 3010, Australia

9. Junzhou Li

   Henan Agricultural University

   Affiliation as printed

   Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou 450046, China

10. Zuoren Yang corresponding

    Chinese Academy of Agricultural Sciences · State Key Laboratory of Cotton Biology

    Affiliation as printed

    State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS) , Anyang 455000, China

11. Xin D. Gao corresponding

    King Abdullah University of Science and Technology

    Affiliation as printed

    Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955, Saudi Arabia

12. Lukasz Kurgan corresponding

    Virginia Commonwealth University

    Affiliation as printed

    Department of Computer Science, Virginia Commonwealth University , Richmond, VA, USA

13. Jiangning Song corresponding

    Monash University

    Affiliation as printed

    Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800, Australia

    Monash Data Future Institutes, Monash University , Melbourne, Victoria 3800, Australia