Bioinformatics, Vol 14, 25-39, Copyright © 1998 by Oxford University Press
J Zhu, JS Liu and CE Lawrence
The selection of a scoring matrix and gap penalty parameters continues to
be an important problem in sequence alignment. We describe here an
algorithm, the 'Bayes block aligner, which bypasses this requirement.
Instead of requiring a fixed set of parameter settings, this algorithm
returns the Bayesian posterior probability for the number of gaps and for
the scoring matrices in any series of interest. Furthermore, instead of
returning the single best alignment for the chosen parameter settings, this
algorithm returns the posterior distribution of all alignments considering
the full range of gapping and scoring matrices selected, weighing each in
proportion to its probability based on the data. We compared the Bayes
aligner with the popular Smith-Waterman algorithm with parameter settings
from the literature which had been optimized for the identification of
structural neighbors, and found that the Bayes aligner correctly identified
more structural neighbors. In a detailed examination of the alignment of a
pair of kinase and a pair of GTPase sequences, we illustrate the
algorithm's potential to identify subsequences that are conserved to
different degrees. In addition, this example shows that the Bayes aligner
returns an alignment-free assessment of the distance between a pair of
sequences.
ARTICLES
Bayesian adaptive sequence alignment algorithms
Wadsworth Center for Laboratories and Research, Albany, NY, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. Satija, L. Pachter, and J. Hein Combining statistical alignment and phylogenetic footprinting to detect regulatory elements Bioinformatics, May 15, 2008; 24(10): 1236 - 1242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Tomovic and E. J. Oakeley Quality estimation of multiple sequence alignments by Bayesian hypothesis testing Bioinformatics, September 15, 2007; 23(18): 2488 - 2490. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kumar and A. Filipski Multiple sequence alignment: In pursuit of homologous DNA positions Genome Res., February 1, 2007; 17(2): 127 - 135. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Huang and D. L. Brutlag Dynamic use of multiple parameter sets in sequence alignment Nucleic Acids Res., January 28, 2007; 35(2): 678 - 686. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. GuhaThakurta Computational identification of transcriptional regulatory elements in DNA sequence Nucleic Acids Res., July 19, 2006; 34(12): 3585 - 3598. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. DING Statistical and Bayesian approaches to RNA secondary structure prediction. RNA, March 1, 2006; 12(3): 323 - 331. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-m. Huang and C. Bystroff Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions Bioinformatics, February 15, 2006; 22(4): 413 - 422. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. OHLER, S. YEKTA, L. P. LIM, D. P. BARTEL, and C. B. BURGE Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification RNA, September 1, 2004; 10(9): 1309 - 1322. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. M. Verghese, Z. Y. Tong, V. Bhagwandin, and G. H. Caughey Mouse Prostasin Gene Structure, Promoter Analysis, and Restricted Expression in Lung and Kidney Am. J. Respir. Cell Mol. Biol., April 1, 2004; 30(4): 519 - 529. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. E. Abbas and S. P. Holmes Bioinformatics and Management Science: Some Common Tools and Techniques Operations Research, March 1, 2004; 52(2): 165 - 190. [Abstract] [PDF]
|
|
|
|
|
|
E. Berezikov, V. Guryev, R. H.A. Plasterk, and E. Cuppen CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting Genome Res., January 1, 2004; 14(1): 170 - 178. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Rombauts, K. Florquin, M. Lescot, K. Marchal, P. Rouze, and Y. Van de Peer Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes Plant Physiology, July 1, 2003; 132(3): 1162 - 1176. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. P. Hare and S. R. Palumbi High Intron Sequence Conservation Across Three Mammalian Orders Suggests Functional Constraints Mol. Biol. Evol., June 1, 2003; 20(6): 969 - 978. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Guo and S. P. Moose Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution PLANT CELL, May 1, 2003; 15(5): 1143 - 1158. [Abstract] [Full Text]
|
|
|
|
 |
|
 M. S. Halfon and A. M. Michelson Exploring genetic regulatory networks in metazoan development: methods and models Physiol Genomics, September 3, 2002; 10(3): 131 - 143. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Konig, J. Burkman, J. Fitzgerald, M. Mitchell, L. Su, and H. Stedman Modular Organization of Phylogenetically Conserved Domains Controlling Developmental Regulation of the Human Skeletal Myosin Heavy Chain Gene Family J. Biol. Chem., July 26, 2002; 277(31): 27593 - 27605. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. T. Dermitzakis and A. G. Clark Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover Mol. Biol. Evol., July 1, 2002; 19(7): 1114 - 1121. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-h. Chiu, C. Amemiya, K. Dewar, C.-B. Kim, F. H. Ruddle, and G. P. Wagner Molecular evolution of the HoxA cluster in the three major gnathostome lineages PNAS, April 16, 2002; 99(8): 5492 - 5497. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B.-J. M. Webb, J. S. Liu, and C. E. Lawrence BALSA: Bayesian algorithm for local sequence alignment Nucleic Acids Res., March 1, 2002; 30(5): 1268 - 1277. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Bergman and M. Kreitman Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences Genome Res., August 1, 2001; 11(8): 1335 - 1345. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. A. McCue, K. A. McDonough, and C. E. Lawrence Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis Genome Res., February 1, 2000; 10(2): 204 - 219. [Abstract] [Full Text]
|
|
|
|
|
|
C.-h. Chiu, C. Amemiya, K. Dewar, C.-B. Kim, F. H. Ruddle, and G. P. Wagner Molecular evolution of the HoxA cluster in the three major gnathostome lineages PNAS, April 16, 2002; 99(8): 5492 - 5497. [Abstract] [Full Text] [PDF]
|
|