Skip to main content

An evolutionary approach for motif discovery and transmembrane protein classification

Tsunoda, Denise F. and Lopes, Heitor S. and Freitas, Alex A. (2005) An evolutionary approach for motif discovery and transmembrane protein classification. In: Rothlauf, Franz, ed. Applications of Evolutionary Computing EvoWorkkshops 2005: EvoBIO, EvoCOMNET, EvoHOT, EvoIASP, EvoMUSART, and EvoSTOC. Lecture Notes in Computer Science . Springer, Berlin, Germany, pp. 105-114. ISBN 978-3-540-25396-9. E-ISBN 978-3-540-32003-6. (doi:10.1007/978-3-540-32003-6_11) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided) (KAR id:14348)

The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided. (Contact us about this Publication)
Official URL
http://dx.doi.org/10.1007/978-3-540-32003-6_11

Abstract

Proteins can be grouped into families according to their biological functions. This paper presents a system, named GAMBIT, which discovers motifs (particular sequences of amino acids) that occur very often in proteins of a given family but rarely occur in proteins of other families. These motifs are used to classify unknown proteins, that is, to predict their function by analyzing the primary structure. To search for motifs in proteins, we developed a GA with specially tailored operators for the problem. GAMBIT was compared with MEME, a web tool for finding motifs in the TransMembrane Protein DataBase. Motifs found by both methods were used to build a decision tree and classification rules, using, respectively, C4.5 and Prism algorithms. Motifs found by GAMBIT led to significantly better results, when compared with those found by MEME, using both classification algorithms.

Item Type: Book section
DOI/Identification number: 10.1007/978-3-540-32003-6_11
Uncontrolled keywords: evolutionary algorithms, bioinformatics, classification
Subjects: Q Science > QA Mathematics (inc Computing science) > QA 76 Software, computer programming,
Divisions: Divisions > Division of Computing, Engineering and Mathematical Sciences > School of Computing
Depositing User: Mark Wheadon
Date Deposited: 24 Nov 2008 18:03 UTC
Last Modified: 16 Feb 2021 12:25 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/14348 (The current URI for this page, for reference purposes)
Freitas, Alex A.: https://orcid.org/0000-0001-9825-4700
  • Depositors only (login required):