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Enriched Bag of Words for Protein Remote Homology Detection

  • Andrea Cucci
  • Pietro Lovato
  • Manuele BicegoEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10029)

Abstract

One of the most challenging Pattern Recognition problems in Bioinformatics is to detect if two proteins that show very low sequence similarity are functionally or structurally related – this is the so-called Protein Remote Homology Detection (PRHD) problem. Even if in this context approaches based on the “Bag of Words” (BoW) paradigm showed high potential, there is still room for further refinements, especially by considering the peculiar application context. In this paper we proposed a modified BoW representation for PRHD, which enriches the classic BoW with information derived from the evolutionary history of mutations each protein is subjected to. An experimental comparison on a standard benchmark demonstrates the feasibility of the proposed technique.

Keywords

Bag of words N-grams Sequence classification 

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Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  1. 1.Dipartimento di Informatica - Ca’ Vignal 2Università degli Studi di VeronaVeronaItaly

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