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NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides
NeuroPred is a web application designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. The user can study one amino acid sequence or multiple sequences simultaneously, selecting from several prediction models and optional, user-defined functions. Logisti...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538825/ https://www.ncbi.nlm.nih.gov/pubmed/16845008 http://dx.doi.org/10.1093/nar/gkl161 |
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author | Southey, Bruce R. Amare, Andinet Zimmerman, Tyler A. Rodriguez-Zas, Sandra L. Sweedler, Jonathan V. |
author_facet | Southey, Bruce R. Amare, Andinet Zimmerman, Tyler A. Rodriguez-Zas, Sandra L. Sweedler, Jonathan V. |
author_sort | Southey, Bruce R. |
collection | PubMed |
description | NeuroPred is a web application designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. The user can study one amino acid sequence or multiple sequences simultaneously, selecting from several prediction models and optional, user-defined functions. Logistic regression models are trained on experimentally verified or published cleavage data from mollusks, mammals and insects, and amino acid motifs reported to be associated with cleavage. Confidence interval limits of the probabilities of cleavage indicate the precision of the predictions; these predictions are transformed into cleavage or non-cleavage events according to user-defined thresholds. In addition to the precursor sequence, NeuroPred accepts user-specified cleavage information, providing model accuracy statistics based on observed and predicted cleavages. Neuropred also computes the mass of the predicted peptides, including user-selectable post-translational modifications. The resulting mass list aids the discovery and confirmation of new neuropeptides using mass spectrometry techniques. The NeuroPred application, manual, reference manuscripts and training sequences are available at . |
format | Text |
id | pubmed-1538825 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-15388252006-08-18 NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides Southey, Bruce R. Amare, Andinet Zimmerman, Tyler A. Rodriguez-Zas, Sandra L. Sweedler, Jonathan V. Nucleic Acids Res Article NeuroPred is a web application designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. The user can study one amino acid sequence or multiple sequences simultaneously, selecting from several prediction models and optional, user-defined functions. Logistic regression models are trained on experimentally verified or published cleavage data from mollusks, mammals and insects, and amino acid motifs reported to be associated with cleavage. Confidence interval limits of the probabilities of cleavage indicate the precision of the predictions; these predictions are transformed into cleavage or non-cleavage events according to user-defined thresholds. In addition to the precursor sequence, NeuroPred accepts user-specified cleavage information, providing model accuracy statistics based on observed and predicted cleavages. Neuropred also computes the mass of the predicted peptides, including user-selectable post-translational modifications. The resulting mass list aids the discovery and confirmation of new neuropeptides using mass spectrometry techniques. The NeuroPred application, manual, reference manuscripts and training sequences are available at . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538825/ /pubmed/16845008 http://dx.doi.org/10.1093/nar/gkl161 Text en © The Author 2006. Published by Oxford University Press. All rights reserved |
spellingShingle | Article Southey, Bruce R. Amare, Andinet Zimmerman, Tyler A. Rodriguez-Zas, Sandra L. Sweedler, Jonathan V. NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
title | NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
title_full | NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
title_fullStr | NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
title_full_unstemmed | NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
title_short | NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
title_sort | neuropred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538825/ https://www.ncbi.nlm.nih.gov/pubmed/16845008 http://dx.doi.org/10.1093/nar/gkl161 |
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