Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (46)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Karplus, K.
Right arrow Articles by Hu, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Karplus, K.
Right arrow Articles by Hu, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 17 no. 8 2001
Pages 713-720
© 2001 Oxford University Press

Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set

Kevin Karplus and Birong Hu

Computer Engineering, University of California, Santa Cruz, CA 59064, USA

Received on February 2, 2001 ; revised on April 11, 2001 ; accepted on May 30, 2001

Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW.

Results: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW.

Availability: The SAM-T99 protocol can be run on the web at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html and the alignment tune-up option described here can be run at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html. The protocol is also part of the standard SAM suite of tools. http://www.cse.ucsc.edu/research/compbio/sam/


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol PlantHome page
L.-R. Zeng, C. H. Park, R.C. Venu, J. Gough, and G.-L. Wang
Classification, Expression Pattern, and E3 Ligase Activity Assay of Rice U-Box-Containing Proteins
Mol Plant, September 1, 2008; 1(5): 800 - 815.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Carroll, W. Beckstead, T. O'Connor, M. Ebbert, M. Clement, Q. Snell, and D. McClellan
DNA reference alignment benchmarks based on tertiary structure of encoded proteins
Bioinformatics, October 1, 2007; 23(19): 2648 - 2649.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
J. Moult
Rigorous performance evaluation in protein structure modelling and implications for computational biology
Phil Trans R Soc B, March 29, 2006; 361(1467): 453 - 458.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. M. Wallace, O. O'Sullivan, D. G. Higgins, and C. Notredame
M-Coffee: combining multiple sequence alignment methods with T-Coffee
Nucleic Acids Res., March 23, 2006; 34(6): 1692 - 1699.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. M. Wallace, O. Orla, and D. G. Higgins
Evaluation of iterative alignment algorithms for multiple alignment
Bioinformatics, April 15, 2005; 21(8): 1408 - 1414.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Nozaki and M. Bellgard
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties
Bioinformatics, April 15, 2005; 21(8): 1421 - 1428.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. V. Stahelin, B. Ananthanarayanan, N. R. Blatner, S. Singh, K. S. Bruzik, D. Murray, and W. Cho
Mechanism of Membrane Binding of the Phospholipase D1 PX Domain
J. Biol. Chem., December 24, 2004; 279(52): 54918 - 54926.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Katoh, K. Misawa, K.-i. Kuma, and T. Miyata
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Nucleic Acids Res., July 15, 2002; 30(14): 3059 - 3066.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. N. Nikolskaya and M. Y. Galperin
A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family
Nucleic Acids Res., June 1, 2002; 30(11): 2453 - 2459.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.