iFeature

a python package and web server for features extraction and selection from protein and peptide sequences

Zhen Chen, Pei Zhao, Fuyi Li, Andre Leier, Tatiana Marquez-Lago, Yanan Wang, Geoffrey I. Webb, A. Ian Smith, Roger J. Daly, Kuo-Chen Chou, Jiangning Song

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Pages (from-to)2499-2502
Number of pages4
JournalBioinformatics
Volume34
Issue number14
DOIs
Publication statusPublished - 15 Jul 2018

Cite this

Chen, Zhen ; Zhao, Pei ; Li, Fuyi ; Leier, Andre ; Marquez-Lago, Tatiana ; Wang, Yanan ; Webb, Geoffrey I. ; Smith, A. Ian ; Daly, Roger J. ; Chou, Kuo-Chen ; Song, Jiangning. / iFeature : a python package and web server for features extraction and selection from protein and peptide sequences. In: Bioinformatics. 2018 ; Vol. 34, No. 14. pp. 2499-2502.
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iFeature : a python package and web server for features extraction and selection from protein and peptide sequences. / Chen, Zhen; Zhao, Pei; Li, Fuyi; Leier, Andre; Marquez-Lago, Tatiana; Wang, Yanan; Webb, Geoffrey I.; Smith, A. Ian; Daly, Roger J.; Chou, Kuo-Chen; Song, Jiangning.

In: Bioinformatics, Vol. 34, No. 14, 15.07.2018, p. 2499-2502.

Research output: Contribution to journalArticleResearchpeer-review

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T2 - a python package and web server for features extraction and selection from protein and peptide sequences

AU - Chen, Zhen

AU - Zhao, Pei

AU - Li, Fuyi

AU - Leier, Andre

AU - Marquez-Lago, Tatiana

AU - Wang, Yanan

AU - Webb, Geoffrey I.

AU - Smith, A. Ian

AU - Daly, Roger J.

AU - Chou, Kuo-Chen

AU - Song, Jiangning

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AB - 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.

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