VacPred: Sequence-based prediction of plant vacuole proteins using machine-learning techniques
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VacPred: Sequence-based prediction of plant vacuole proteins using machine-learning techniques ARVIND KUMAR YADAV1, and DEEPAK SINGLA2*, 1
Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh 173 234, India
2
School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141 004, India *Corresponding author (Email, [email protected])
Equal contribution.
MS received 12 March 2020; accepted 30 July 2020 Subcellular localization prediction of the proteome is one of major goals of large-scale genome or proteome sequencing projects to define the gene functions that could be possible with the help of computational modeling techniques. Previously, different methods have been developed for this purpose using multi-label classification system and achieved a high level of accuracy. However, during the validation of our blind dataset of plant vacuole proteins, we observed that they have poor performance with accuracy value range from *1.3% to 48.5%. The results showed that the previously developed methods are not very accurate for the plant vacuole protein prediction and thus emphasize the need to develop a more accurate and reliable algorithm. In this study, we have developed various compositions as well as PSSM-based models and achieved a high accuracy than previously developed methods. We have shown that our best model achieved *63% accuracy on blind dataset, which is far better than currently available tools. Furthermore, we have implemented our best models in the form of GUI-based free software called ‘VacPred’ which is compatible with both Linux and Window platform. This software is freely available for download at www.deepaklab.com/vacpred. Keywords.
Software; subcellular localization; support vector machine; vacuole
1. Introduction Vacuoles represent the cellular component of any living cell that varies in size and shape (Zhang et al. 2014a). Plant vacuole is represented by a single large structure that is involved in diverse functions such as plant growth and development, maintaining cellular homeostasis, cellular function to retaining turgor and nutrients, ions and secondary metabolites accretion (Pereira et al. 2014). Inside the seeds, the vacuole acts as the storage site of proteins and carbohydrates, various kinds of flavonoids for flower and fruit color, and is also associated with cellular response to the environment (Grotewold 2006; Marty 1999; Park et al. 2004). Vacuole proteins
function as a transporter to transport diverse class of ions, sugars, amino acids, and other molecules (Zhang et al. 2015). Lytic vacuole plays significant role in the degradation of cellular waste, defence, and program cell death (Ibl and Stoger 2014; Shimada et al. 2018). With the availability of the whole genome or proteome of any plant, the ultimate goal is their fast and accurate functional assignment which depends upon the subcellular location of the proteins. The e
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