Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations

Simple item page
dc.contributor.authorSzafron, Duane
dc.contributor.authorLu, Paul
dc.contributor.authorGreiner, Russell
dc.contributor.authorWishart, David S.
dc.contributor.authorPoulin, Brett
dc.contributor.authorEisner, Roman
dc.contributor.authorLu, Zhiyong
dc.contributor.authorAnvik, John
dc.contributor.authorMacdonell, Cam
dc.contributor.authorFyshe, Alona
dc.contributor.authorMeeuwis, David
dc.date.accessioned2019-09-03T22:08:08Z
dc.date.available2019-09-03T22:08:08Z
dc.date.issued2004
dc.descriptionSherpa Romeo green journal. Permission to archive final published version.en_US
dc.description.abstractProteome Analyst (PA) (http://www.cs.ualberta.ca/~bioinfo/PA/) is a publicly available, high-throughput, web-based system for predicting various properties of each protein in an entire proteome. Using machine-learned classifiers, PA can predict, for example, the GeneQuiz general function and Gene Ontology (GO) molecular function of a protein. In addition, PA is currently the most accurate and most comprehensive system for predicting subcellular localization, the location within a cell where a protein performs its main function. Two other capabilities of PA are notable. First, PA can create a custom classifier to predict a new property, without requiring any programming, based on labeled training data (i.e. a set of examples, each with the correct classification label) provided by a user. PA has been used to create custom classifiers for potassium-ion channel proteins and other general function ontologies. Second, PA provides a sophisticated explanation feature that shows why one prediction is chosen over another. The PA system produces a Naïve Bayes classifier, which is amenable to a graphical and interactive approach to explanations for its predictions; transparent predictions increase the user's confidence in, and understanding of, PA.en_US
dc.description.peer-reviewYesen_US
dc.identifier.citationSzafron, D., Lu, P., Greiner, R., Wishart, D. S., Poulin, B. Eisner, R., ... Meeuwis, D. (2004). Proteome Analyst: Custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Research, 32(2), Pages W365–W371, https://doi.org/10.1093/nar/gkh485en_US
dc.identifier.urihttps://hdl.handle.net/10133/5543
dc.language.isoen_USen_US
dc.publisherOxford University Pressen_US
dc.publisher.departmentDepartment of Mathematics and Computer Scienceen_US
dc.publisher.facultyArts and Scienceen_US
dc.publisher.institutionUniversity of Albertaen_US
dc.publisher.institutionUniversity of Lethbridgeen_US
dc.publisher.urlhttps://doi.org/10.1093/nar/gkh485en_US
dc.subjectProteome Analysten_US
dc.subjectCustom predictions
dc.subjectCustom classifiers
dc.subjectProteome annotations
dc.subject.lcshProteomics
dc.subject.lcshProteins
dc.titleProteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotationsen_US
dc.typeArticleen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Anvik-proteome-analyst.pdf
Size:
329.17 KB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
1.75 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Anvik, John