Context sensitive vocabulary and its application in protein secondary structure prediction

Yan Liu, Jaime Carbonell, Judith Klein-Seetharaman, Vanathi Gooalakrishnan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Scopus citations

Abstract

Protein secondary structure prediction is an important step towards understanding the relation between protein sequence and structure. However, most current prediction methods use features difficult for biologists to interpret. In this paper, we present a new method that applies information retrieval techniques to solve the problem: we extract a context sensitive biological vocabulary for protein sequences and apply text classification methods to predict protein secondary structure. Experimental results show that our method performs comparably to the state-of-art methods. Furthermore, the context sensitive vocabularies can serve as a useful tool to discover meaningful regular expression patterns for protein structures.

Original languageEnglish (US)
Title of host publicationProceedings of Sheffield SIGIR - Twenty-Seventh Annual International ACM SIGIR Conference on Research and Development in Information Retrieval
PublisherAssociation for Computing Machinery (ACM)
Pages538-539
Number of pages2
ISBN (Print)1581138814, 9781581138818
DOIs
StatePublished - 2004
Externally publishedYes
EventProceedings of Sheffield SIGIR - Twenty-Seventh Annual International ACM SIGIR Conference on Research and Development in Information Retrieval - Sheffield, United Kingdom
Duration: Jul 25 2004Jul 29 2004

Publication series

NameProceedings of Sheffield SIGIR - Twenty-Seventh Annual International ACM SIGIR Conference on Research and Development in Information Retrieval

Conference

ConferenceProceedings of Sheffield SIGIR - Twenty-Seventh Annual International ACM SIGIR Conference on Research and Development in Information Retrieval
Country/TerritoryUnited Kingdom
CitySheffield
Period7/25/047/29/04

Keywords

  • Biological language
  • Context Sensitive Vocabulary
  • Protein secondary structure prediction

ASJC Scopus subject areas

  • Engineering(all)

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