title: POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors.
abstract: BACKGROUND
  At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences. Frequently the most accurate classifiers are obtained by training support vector machines (SVMs) with complex sequence kernels. However, a cumbersome shortcoming of SVMs is that their learned decision rules are very hard to understand for humans and cannot easily be related to biological facts.
  
  
  RESULTS
  To make SVM-based sequence classifiers more accessible and profitable, we introduce the concept of positional oligomer importance matrices (POIMs) and propose an efficient algorithm for their computation. In contrast to the raw SVM feature weighting, POIMs take the underlying correlation structure of k-mer features induced by overlaps of related k-mers into account. POIMs can be seen as a powerful generalization of sequence logos: they allow to capture and visualize sequence patterns that are relevant for the investigated biological phenomena.
  
  
  BACKGROUND
  All source code, datasets, tables and figures are available at http://www.fml.tuebingen.mpg.de/raetsch/projects/POIM.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Fraunhofer Institute FIRST, Department IDA, Kekulèstr. 7, 12489 Berlin, Germany. Soeren.Sonnenburg@first.fraunhofer.de
authors.forename: Sören
authors.initials: S
authors.lastname: Sonnenburg
authors.forename: Alexander
authors.initials: A
authors.lastname: Zien
authors.forename: Petra
authors.initials: P
authors.lastname: Philips
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA