de.mpg.escidoc.pubman.appbase.FacesBean
English
 
Help Guide Disclaimer Contact us Login
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

Protein homology detection using string alignment kernels

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons84183

Saigo,  H
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

Locator
There are no locators available
Fulltext (public)
There are no public fulltexts available
Supplementary Material (public)
There is no public supplementary material available
Citation

Saigo, H., Vert J-P, Ueda, N., & Akutsu, T. (2004). Protein homology detection using string alignment kernels. Bioinformatics, 20(11), 1682-1689. doi:10.1093/bioinformatics/bth141.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0013-F3D1-3
Abstract
Remote homology detection between protein sequences is a central problem in computational biology. Discriminative methods involving support vector machines (SVM) are currently the most effective methods for the problem of superfamily recognition in the SCOP database. The performance of SVMs depend critically on the kernel function used to quantify the similarity between sequences. We propose new kernels for strings adapted to biological sequences, which we call local alignment kernels. These kernels measure the similarity between two sequences by summing up scores obtained from local alignments with gaps of the sequences. When tested in combination with SVM on their ability to recognize SCOP superfamilies on a benchmark dataset, the new kernels outperform state-of-the art methods for remote homology detection.