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PSCL: Predicting protein subcellular localization based on optimal functional domains
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نویسنده
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wang k. ,hu l.-l. ,shi x.-h. ,dong y.-s. ,li h.-p. ,wen t.-q.
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منبع
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protein and peptide letters - 2012 - دوره : 19 - شماره : 1 - صفحه:15 -22
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چکیده
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It is well known that protein subcellular localizations are closely related to their functions. although many computational methods and tools are available from internet,it is still necessary to develop new algorithms in this filed to gain a better understanding of the complex mechanism of plant subcellular localization. here,we provide a new web server named pscl for plant protein subcellular localization prediction by employing optimized functional domains. after feature optimization,848 optimal functional domains from interpro were obtained to represent each protein. by calculating the distances to each of the seven categories,pscl showing the possibilities of a protein located into each of those categories in ascending order. toward our dataset,pscl achieved a first-order predicted accuracy of 75.7% by jackknife test. gene ontology enrichment analysis showing that catalytic activity,cellular process and metabolic process are strongly correlated with the localization of plant proteins. finally,pscl,a linux operate system based web interface for the predictor was designed and is accessible for public use at http://pscl.biosino. org/. © 2012 bentham science publishers.
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کلیدواژه
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Incremental feature selection (IFS); Jackknife test; Minimum redundancy maximum relevance (mRMR); Nearest neighbor algorithm; Optimal functional domains; Protein subcellular localization
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آدرس
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laboratory of molecular neurobiology,school of life sciences,shanghai university,no.99 shangda rd.,shanghai 200444,china,institute of systems biology,shanghai university, China, institute of systems biology,shanghai university,shanghai 200444,china,department of chemistry,college of sciences,shanghai university, China, institute of health sciences,shanghai institutes for biological sciences (sibs),chinese academy of sciences (cas),shanghai,china,shanghai jiao tong university school of medicine (sjtusm), China, department of life science and technology,huazhong university of science and technology, China, cas-mpg partner institute for computational biology,shanghai institutes for biological sciences, China, laboratory of molecular neurobiology,school of life sciences,shanghai university,no.99 shangda rd.,shanghai 200444,china,institute of systems biology,shanghai university, China
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Authors
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