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...
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| Veröffentlicht in: | Nucleic acids research 2006-07, Vol.34 (suppl-2), p.W267-W272 |
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| container_issue | suppl-2 |
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| container_title | Nucleic acids research |
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| creator | Southey, Bruce R. Amare, Andinet Zimmerman, Tyler A. Rodriguez-Zas, Sandra L. Sweedler, Jonathan V. |
| 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 http://neuroproteomics.scs.uiuc.edu/neuropred.html. |
| doi_str_mv | 10.1093/nar/gkl161 |
| format | Article |
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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 http://neuroproteomics.scs.uiuc.edu/neuropred.html.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkl161</identifier><identifier>PMID: 16845008</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Internet ; Logistic Models ; Mass Spectrometry ; Mollusca ; Neuropeptides - chemistry ; Neuropeptides - metabolism ; Protein Precursors - chemistry ; Protein Precursors - metabolism ; Sequence Analysis, Protein ; Software ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2006-07, Vol.34 (suppl-2), p.W267-W272</ispartof><rights>The Author 2006. Published by Oxford University Press. All rights reserved The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org</rights><rights>Copyright Oxford University Press(England) 2006</rights><rights>The Author 2006. Published by Oxford University Press. 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Acids Res</addtitle><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 http://neuroproteomics.scs.uiuc.edu/neuropred.html.</description><subject>Animals</subject><subject>Internet</subject><subject>Logistic Models</subject><subject>Mass Spectrometry</subject><subject>Mollusca</subject><subject>Neuropeptides - chemistry</subject><subject>Neuropeptides - metabolism</subject><subject>Protein Precursors - chemistry</subject><subject>Protein Precursors - metabolism</subject><subject>Sequence Analysis, Protein</subject><subject>Software</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkk1v1DAQhi0Eokvhwg9AEQcOSKEef8XhUAktH0WqgAOIqhfLyU62brNxsJ0F_j0Ouyofl73YemeeGY1evYQ8BvoCaM1PBhtO1jc9KLhDFsAVK0Wt2F2yoJzKEqjQR-RBjNeUggAp7pMjUFpISvWCfP-AU_CfAq5eFrZI3vf5KcasXZuKtke7tWssoksYCzcUw4yPOCa3whlrpxB9iIUdVln67VxOV1hsbIx5wne_VcA49ckN62I_Gh-Se53tIz7a_8fky9s3n5dn5fnHd--Xr87LVtYqlVVjtYYObMsrxjuslba5wRXVyKGtVCcaDUwiFx3lrOtyoaKMN0JVTQ2UH5PT3d5xaja4anFIwfZmDG5jw0_jrTP_dgZ3ZdZ-a0ByrZnMC57tFwT_bcKYzMbFFvveDuinaJRWQihgB0EGTFCm9UEQaq4kU3UGn_4HXvspDNkuwyhVnHIlDkCy0sDn257voDb4GAN2twYANXOGTM6Q2WUow0_-tuwPug9NBsod4GLCH7d9G26MqnglzdnFpamrr6-X6kKaS_4LiV7SuQ</recordid><startdate>20060701</startdate><enddate>20060701</enddate><creator>Southey, Bruce R.</creator><creator>Amare, Andinet</creator><creator>Zimmerman, Tyler A.</creator><creator>Rodriguez-Zas, Sandra L.</creator><creator>Sweedler, Jonathan V.</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20060701</creationdate><title>NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides</title><author>Southey, Bruce R. ; Amare, Andinet ; Zimmerman, Tyler A. ; Rodriguez-Zas, Sandra L. ; Sweedler, Jonathan V.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c596t-7ba881f1ac3723fe968a5963608e31c76f4b8125e34f032ff6f47023b467b9103</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Animals</topic><topic>Internet</topic><topic>Logistic Models</topic><topic>Mass Spectrometry</topic><topic>Mollusca</topic><topic>Neuropeptides - chemistry</topic><topic>Neuropeptides - metabolism</topic><topic>Protein Precursors - chemistry</topic><topic>Protein Precursors - metabolism</topic><topic>Sequence Analysis, Protein</topic><topic>Software</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Southey, Bruce R.</creatorcontrib><creatorcontrib>Amare, Andinet</creatorcontrib><creatorcontrib>Zimmerman, Tyler A.</creatorcontrib><creatorcontrib>Rodriguez-Zas, Sandra L.</creatorcontrib><creatorcontrib>Sweedler, Jonathan V.</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Southey, Bruce R.</au><au>Amare, Andinet</au><au>Zimmerman, Tyler A.</au><au>Rodriguez-Zas, Sandra L.</au><au>Sweedler, Jonathan V.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucl. Acids Res</addtitle><date>2006-07-01</date><risdate>2006</risdate><volume>34</volume><issue>suppl-2</issue><spage>W267</spage><epage>W272</epage><pages>W267-W272</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>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. 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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Internet Logistic Models Mass Spectrometry Mollusca Neuropeptides - chemistry Neuropeptides - metabolism Protein Precursors - chemistry Protein Precursors - metabolism Sequence Analysis, Protein Software User-Computer Interface |
| title | NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides |
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