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Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence

BACKGROUND: Knowing the submitochondria localization of a mitochondria protein is an important step to understand its function. We develop a method which is based on an extended version of pseudo-amino acid composition to predict the protein localization within mitochondria. This work goes one step...

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Detalles Bibliográficos
Autores principales: Du, Pufeng, Li, Yanda
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716183/
https://www.ncbi.nlm.nih.gov/pubmed/17134515
http://dx.doi.org/10.1186/1471-2105-7-518
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author Du, Pufeng
Li, Yanda
author_facet Du, Pufeng
Li, Yanda
author_sort Du, Pufeng
collection PubMed
description BACKGROUND: Knowing the submitochondria localization of a mitochondria protein is an important step to understand its function. We develop a method which is based on an extended version of pseudo-amino acid composition to predict the protein localization within mitochondria. This work goes one step further than predicting protein subcellular location. We also try to predict the membrane protein type for mitochondrial inner membrane proteins. RESULTS: By using leave-one-out cross validation, the prediction accuracy is 85.5% for inner membrane, 94.5% for matrix and 51.2% for outer membrane. The overall prediction accuracy for submitochondria location prediction is 85.2%. For proteins predicted to localize at inner membrane, the accuracy is 94.6% for membrane protein type prediction. CONCLUSION: Our method is an effective method for predicting protein submitochondria location. But even with our method or the methods at subcellular level, the prediction of protein submitochondria location is still a challenging problem. The online service SubMito is now available at:
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spelling pubmed-17161832006-12-28 Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence Du, Pufeng Li, Yanda BMC Bioinformatics Methodology Article BACKGROUND: Knowing the submitochondria localization of a mitochondria protein is an important step to understand its function. We develop a method which is based on an extended version of pseudo-amino acid composition to predict the protein localization within mitochondria. This work goes one step further than predicting protein subcellular location. We also try to predict the membrane protein type for mitochondrial inner membrane proteins. RESULTS: By using leave-one-out cross validation, the prediction accuracy is 85.5% for inner membrane, 94.5% for matrix and 51.2% for outer membrane. The overall prediction accuracy for submitochondria location prediction is 85.2%. For proteins predicted to localize at inner membrane, the accuracy is 94.6% for membrane protein type prediction. CONCLUSION: Our method is an effective method for predicting protein submitochondria location. But even with our method or the methods at subcellular level, the prediction of protein submitochondria location is still a challenging problem. The online service SubMito is now available at: BioMed Central 2006-11-30 /pmc/articles/PMC1716183/ /pubmed/17134515 http://dx.doi.org/10.1186/1471-2105-7-518 Text en Copyright © 2006 Du and Li; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Du, Pufeng
Li, Yanda
Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
title Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
title_full Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
title_fullStr Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
title_full_unstemmed Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
title_short Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
title_sort prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716183/
https://www.ncbi.nlm.nih.gov/pubmed/17134515
http://dx.doi.org/10.1186/1471-2105-7-518
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