PyFeat: A Python-based effective feature generation tool for DNA, RNA and protein sequences

Rafsanjani Muhammod, Sajid Ahmed, Dewan Md Farid, Swakkhar Shatabda, Alok Sharma, Abdollah Dehzangi

Research output: Contribution to journalArticlepeer-review

41 Scopus citations

Abstract

Motivation: Extracting useful feature set which contains significant discriminatory information is a critical step in effectively presenting sequence data to predict structural, functional, interaction and expression of proteins, DNAs and RNAs. Also, being able to filter features with significant information and avoid sparsity in the extracted features require the employment of efficient feature selection techniques. Here we present PyFeat as a practical and easy to use toolkit implemented in Python for extracting various features from proteins, DNAs and RNAs. To build PyFeat we mainly focused on extracting features that capture information about the interaction of neighboring residues to be able to provide more local information. We then employ AdaBoost technique to select features with maximum discriminatory information. In this way, we can significantly reduce the number of extracted features and enable PyFeat to represent the combination of effective features from large neighboring residues. As a result, PyFeat is able to extract features from 13 different techniques and represent context free combination of effective features. The source code for PyFeat standalone toolkit and employed benchmarks with a comprehensive user manual explaining its system and workflow in a step by step manner are publicly available. Results: https://github.com/mrzResearchArena/PyFeat/blob/master/RESULTS.md. Availability and implementation: Toolkit, source code and manual to use PyFeat: https://github. com/mrzResearchArena/PyFeat/.

Original languageEnglish (US)
Pages (from-to)3831-3833
Number of pages3
JournalBioinformatics
Volume35
Issue number19
DOIs
StatePublished - Oct 1 2019
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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