Access

You are not currently logged in.

Access your personal account or get JSTOR access through your library or other institution:

login

Log in to your personal account or through your institution.

If you need an accessible version of this item please contact JSTOR User Support

A Bayesian Insertion/Deletion Algorithm for Distant Protein Motif Searching via Entropy Filtering

Jun Xie, Ker-Chau Li and Minou Bina
Journal of the American Statistical Association
Vol. 99, No. 466 (Apr., 2004), pp. 409-420
Stable URL: http://www.jstor.org/stable/27590397
Page Count: 12
  • Get Access
  • Download ($14.00)
  • Cite this Item
If you need an accessible version of this item please contact JSTOR User Support
A Bayesian Insertion/Deletion Algorithm for Distant Protein Motif Searching via Entropy Filtering
Preview not available

Abstract

Bayesian models have been developed that find ungapped motifs in multiple protein sequences. In this article, we extend the model to allow for deletions and insertions in motifs. Direct generalization of the ungapped algorithm, based on Gibbs sampling, proved unsuccessful because the configuration space became much larger. To alleviate the convergence difficulty, a two-stage procedure is introduced. At the first stage, we develop a method called entropy filtering, which quickly searchs "good" starting points for the alignment approach without the concern of deletion/insertion patterns. At the second stage, we switch to an algorithm that generates both a random vector that represents insertion/deletion patterns and a random variable of motif locations. After the two steps, gapped-motif alignments are obtained for multiple sequences. When applied to datasets that consist of helix—loop—helix proteins and high mobility group proteins, respectively, our methods show great improvements over those that produce ungapped alignments.

Page Thumbnails

  • Thumbnail: Page 
409
    409
  • Thumbnail: Page 
410
    410
  • Thumbnail: Page 
411
    411
  • Thumbnail: Page 
412
    412
  • Thumbnail: Page 
413
    413
  • Thumbnail: Page 
414
    414
  • Thumbnail: Page 
415
    415
  • Thumbnail: Page 
416
    416
  • Thumbnail: Page 
417
    417
  • Thumbnail: Page 
418
    418
  • Thumbnail: Page 
419
    419
  • Thumbnail: Page 
420
    420