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In biochemistry, a hypothetical protein is a protein whose existence has been predicted, but for which there is a lack of experimental evidence that it is expressed in vivo. Sequencing of several genomes has resulted in numerous predicted open reading frames to which functions cannot be readily assigned.
- Construction of Datasets
- Significance of The Features
- Classifier Design and Training
- Performance Evaluation
- GeneratedCaptionsTabForHeroSec
Two datasets were prepared for this study, viz. positive and negative datasets, with the former constituting the HPs while the latter representing functional proteins. The final dataset consisted of 106 positive instances and 194 negative instances of HPs. These proteins were considered from GenBank with keyword searches “Homo sapiens” AND “Hypothe...
The six features from our earlier proposed six-point classification scoring schema are pfam score, orthology inference, functional linkages, back-to-back orthology, subcellular location and protein associations taken from known databases and visualizers . Conservation is one of the important features of essential proteins. Studies have proven that ...
Prediction of the function of HPs can be presented as a binary classification problem. Each protein from both datasets was annotated across nine selected features and assigned a score of 1 if the protein met the criteria or 0 if it did not (Fig. 2). Criteria followed for scoring are shown in Additional file 5: Figure S1. The classifier was trained ...
Evaluating the performance of learning algorithms is a central aspect of machine learning. Several measures including cross-validation as a standard method and a 10-fold cross-validation using WEKA were applied to test the performance of the predictive model. To mitigate the over-fitting problem, the following measures were used to evaluate the pe...
This article presents a nine-point classification scoring schema to annotate the function of hypothetical proteins based on sequence-, topological- and structure-based features. The article also compares the performance of different machine learning algorithms and introduces three new features: pseudogenes, homology modelling and non-coding RNAs.
- Johny Ijaq, Girik Malik, Anuj Kumar, Partha Sarathi Das, Narendra Meena, Neeraja Bethi, Vijayaraghav...
- 2019
29 de dez. de 2006 · This method can identify functionally linked proteins with no amino acid sequence similarity so that the function of the hypothetical protein can be known. This method was tested using three proteins the ribosome protein RL7 and the flagellar structural protein FlgL, as well as a protein known to participate in a metabolic pathway ...
- Selvarajan Sivashankari, Piramanayagam Shanmughavel
- 2006
30 de mar. de 2015 · This article reviews various methods and techniques for predicting and validating the functions of hypothetical proteins (HPs), which are proteins with no experimental evidence of translation. It also discusses the challenges and opportunities of using next generation sequencing (NGS) for HPs annotation and characterization.
Hypothetical protein is a term used for proteins that have not been characterized or functionally annotated. Learn about the types, functions and examples of hypothetical proteins in genomics, parasitology and microbiology.
1 de set. de 2005 · There is so far no classification of hypothetical proteins (HPs) and working terms are replacing definitions of hypothetical proteins. In the strict sense, HPs are predicted proteins, proteins predicted from nucleic acid sequences and that have not been shown to exist by experimental protein chemical evidence.
Abstract. A large part of mammalian proteomes is represented by hypothetical proteins (HP), i.e. proteins predicted from nucleic acid sequences only and protein sequences with unknown function. Databases are far from being complete and errors are expected.
