A Computational Method for Predicting Fluorescent Proteins

A protein and fluorescent technology, applied in computing, computer components, instruments, etc., can solve the problems of unsuitable proteome analysis and low efficiency, and achieve the effect of improving prediction accuracy, improving correctness, and enhancing generalization performance

Active Publication Date: 2022-02-01
XINYANG NORMAL UNIVERSITY
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  • Abstract
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  • Claims
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AI Technical Summary

Problems solved by technology

Although analyzing protein structure can effectively understand protein function, this method is too inefficient to be suitable for large-scale proteome analysis

Method used

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  • A Computational Method for Predicting Fluorescent Proteins
  • A Computational Method for Predicting Fluorescent Proteins
  • A Computational Method for Predicting Fluorescent Proteins

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] S1: Feature calculation

[0044] Given a set of protein sequences: the present invention searches for fluorescent proteins with the keyword "bioluminescent proteins" from the Uniprot data (https: / / www.uniprot.org / ), and removes those with the word "bioluminescent" in the description from the remaining proteins Proteins constitute non-fluorescent proteins; then use the blastclust program to perform de-redundancy operations to obtain fluorescent proteins and non-fluorescent proteins with a homologous similarity of less than 30% to form a benchmark data set; for any protein sequence P (the protein is composed of N amino acid residues), according to the analysis of the biological, physical and chemical properties of the fluorescent protein, calculate the characteristics related to the fluorescence;

[0045] Fluorescence-associated features include:

[0046] (1) Amino acid composition characteristics, using Composition Profiler (download URL: http: / / www.cprofiler.org / ) to c...

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Abstract

The invention belongs to the fields of bioinformatics, data mining and intelligent computing, and in particular relates to a calculation-based method for predicting fluorescent proteins. Including the following steps: S1: According to the biological, physical, and chemical property analysis of fluorescent proteins, calculate the characteristics related to fluorescence; S2: For the constructed feature vector, calculate the correlation score between each feature value and the protein type label and sort : S3: Use the incremental feature selection strategy to select the sorted features to build the optimal feature subset; S4: Use the Bagging learning strategy to build a variety of learning models based on different training samples for prediction. The prediction method of the invention has higher accuracy and better generalization, and can greatly improve prediction efficiency.

Description

technical field [0001] The invention belongs to the fields of bioinformatics, data mining and intelligent computing, and in particular relates to a calculation-based method for predicting fluorescent proteins. Background technique [0002] Fluorescent protein is a kind of special protein that can emit light by itself widely in nature, and it is distributed in many living tissues or organs. Compared to other proteins, fluorescent proteins can convert chemical energy into light energy. Because fluorescence is easy to observe, fluorescent proteins can be widely used in various aspects of biological research, such as bioluminescent images, biosensors, environmental detectors, etc. In particular, biologists can engineer fluorescent proteins into "marker proteins" for in-depth proteomics experiments. In cancer or tumor research, fluorescent proteins are often used to record the development of diseased tissues, the growth, invasion and metastasis of tumor cells. In 2008, Japanes...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B5/00G16B25/10G16B30/10G06K9/62
CPCG16B5/00G16B25/10G16B30/10G06F18/2411G06F18/214
Inventor 张健张馨艺何水龙
Owner XINYANG NORMAL UNIVERSITY
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