iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

• Published in: Bioinformatics Vol. 34; no. 14; pp. 2499 - 2502
• Main Authors: Chen, Zhen, Zhao, Pei, Li, Fuyi, Leier, André, Marquez-Lago, Tatiana T, Wang, Yanan, Webb, Geoffrey I, Smith, A Ian, Daly, Roger J, Chou, Kuo-Chen, Song, Jiangning
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.07.2018
• Subjects: Applications Notes; Machine Learning; Molecular Sequence Annotation; Peptides - chemistry; Peptides - metabolism; Peptides - physiology; Protein Conformation; Proteins - chemistry; Proteins - metabolism; Proteins - physiology; Sequence Analysis, Protein - methods; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bty140

Abstract Summary Structural and physiochemical descriptors extracted from sequence data have been widely used to represent sequences and predict structural, functional, expression and interaction profiles of proteins and peptides as well as DNAs/RNAs. Here, we present iFeature, a versatile Python-based toolkit for generating various numerical feature representation schemes for both protein and peptide sequences. iFeature is capable of calculating and extracting a comprehensive spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. It also allows users to extract specific amino acid properties from the AAindex database. Furthermore, iFeature integrates 12 different types of commonly used feature clustering, selection and dimensionality reduction algorithms, greatly facilitating training, analysis and benchmarking of machine-learning models. The functionality of iFeature is made freely available via an online web server and a stand-alone toolkit. Availability and implementation http://iFeature.erc.monash.edu/; https://github.com/Superzchen/iFeature/. Supplementary information Supplementary data are available at Bioinformatics online.