An HMM posterior decoder for sequence feature prediction that includes homology information
1Center for Genomics and Bioinformatics, Karolinska Institutet SE-17 177 Stockholm, Sweden
2The Bioinformatics Center, University of Copenhagen Universitetsparken 15, DK-2100 Copenhagen, Denmark
*To whom correspondence should be addressed.
Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil–coil structures, protein secondary structure or genes, extra support can be gained from homologs.
Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines probabilities for sequence features of homologs by considering the average of the posterior label probability of each position in a global sequence alignment. The algorithm is an extension of the previously described ‘optimal accuracy’ decoder, allowing homology information to be used. It was benchmarked using an HMM for transmembrane topology and signal peptide prediction, Phobius. We found that the performance was substantially increased when incorporating information from homologs.
Availability: A prediction server for transmembrane topology and signal peptides that uses the algorithm is available at http://phobius.cgb.ki.se/poly.html. An implementation of the algorithm is available on request from the authors.
Contact: Erik.Sonnhammer{at}cgb.ki.se
Received on January 17, 2005; accepted on March 27, 2005
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. A. Mihindukulasuriya, G. Wu, J. St. Leger, R. W. Nordhausen, and D. Wang Identification of a Novel Coronavirus from a Beluga Whale by Using a Panviral Microarray J. Virol., May 15, 2008; 82(10): 5084 - 5088. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Pirovano, K. A. Feenstra, and J. Heringa PRALINETM: a strategy for improved multiple alignment of transmembrane proteins Bioinformatics, February 15, 2008; 24(4): 492 - 497. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Lunter, A. Rocco, N. Mimouni, A. Heger, A. Caldeira, and J. Hein Uncertainty in homology inferences: Assessing and improving genomic sequence alignment Genome Res., February 1, 2008; 18(2): 298 - 309. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Papaloukas, E. Granseth, H. Viklund, and A. Elofsson Estimating the length of transmembrane helices using Z-coordinate predictions Protein Sci., February 1, 2008; 17(2): 271 - 278. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Nystedt, A. C. Frank, M. Thollesson, and S. G. E. Andersson Diversifying Selection and Concerted Evolution of a Type IV Secretion System in Bartonella Mol. Biol. Evol., February 1, 2008; 25(2): 287 - 300. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Rossignol, P. Lechat, C. Cuomo, Q. Zeng, I. Moszer, and C. d'Enfert CandidaDB: a multi-genome database for Candida species and related Saccharomycotina Nucleic Acids Res., January 11, 2008; 36(suppl_1): D557 - D561. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Guo and J. Kim Molecular Evolution of Drosophila Odorant Receptor Genes Mol. Biol. Evol., May 1, 2007; 24(5): 1198 - 1207. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. T. Jones Improving the accuracy of transmembrane protein topology prediction using evolutionary information Bioinformatics, March 1, 2007; 23(5): 538 - 544. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. G. Kreft, L. Wang, and M. Hochstrasser Membrane Topology of the Yeast Endoplasmic Reticulum-localized Ubiquitin Ligase Doa10 and Comparison with Its Human Ortholog TEB4 (MARCH-VI) J. Biol. Chem., February 24, 2006; 281(8): 4646 - 4653. [Abstract] [Full Text] [PDF]
|
|