Qualitative and quantitative analysis of peptide microarray binding experiments using SVM-PEPARRAY

Gang Chen, Zhixiang Zuo, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, Tongbin Li

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Abstract

A main objective of analyzing peptide array-based binding experiments is to uncover the relationship between a peptide sequence and the binding outcome. Limited by the peptide array technologies available for applications, few attempts have been made to construct qualitative or quantitative models that depict the peptide sequence:binding strength relationships in peptide microarray-based binding studies. There has been a long history of similar modeling efforts based on low-throughput binding data in the areas of T-cell epitope screening and kinase substrate mapping, however. The keen needs in peptide array applications and the success of the modeling efforts in related fields have prompted us to develop SVM-PEPARRAY, a Web-based program capable of constructing qualitative and quantitative models based on peptide microarray binding datasets using support vector machine (SVM) modeling methods. We expect that such modeling analysis will allow researchers to quickly extract sequence-based biological information from improved peptide array binding results and provide more precise and accurate information about the biological systems investigated.

Original languageEnglish (US)
Title of host publicationPeptide Microarrays
Subtitle of host publicationMethods and Protocols
EditorsMarina Cretich, Marcella Chiari
Pages403-411
Number of pages9
DOIs
StatePublished - 2009

Publication series

NameMethods in Molecular Biology
Volume570
ISSN (Print)1064-3745

Keywords

  • SVM
  • SVM-PEPARRAY
  • SVR
  • modeling
  • on-chip binding experiment

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