title: Classification of protein sequences by means of irredundant patterns.
abstract: BACKGROUND
  The classification of protein sequences using string algorithms provides valuable insights for protein function prediction. Several methods, based on a variety of different patterns, have been previously proposed. Almost all string-based approaches discover patterns that are not "independent, " and therefore the associated scores overcount, a multiple number of times, the contribution of patterns that cover the same region of a sequence.
  
  
  RESULTS
  In this paper we use a class of patterns, called irredundant, that is specifically designed to address this issue. Loosely speaking the set of irredundant patterns is the smallest class of "independent" patterns that can describe all common patterns in two sequences, thus they avoid overcounting. We present a novel discriminative method, called Irredundant Class, based on the statistics of irredundant patterns combined with the power of support vector machines.
  
  
  CONCLUSIONS
  Tests on benchmark data show that Irredundant Class outperforms most of the string algorithms previously proposed, and it achieves results as good as current state-of-the-art methods. Moreover the footprints of the most discriminative irredundant patterns can be used to guide the identification of functional regions in protein sequences.
authors.affiliation: Department of Information Engineering, University of Padova, Italy. ciompin@dei.unipd.it
authors.forename: Matteo
authors.initials: M
authors.lastname: Comin
authors.forename: Davide
authors.initials: D
authors.lastname: Verzotto
mesh_terms: D000465:Algorithms; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins