Bioinformatics, Vol 15, 211-218, Copyright © 1999 by Oxford University Press
B Morgenstern
MOTIVATION: The performance and time complexity of an improved version of
the segment-to-segment approach to multiple sequence alignment is
discussed. In this approach, alignments are composed from gap-free segment
pairs, and the score of an alignment is defined as the sum of so-called
weights of these segment pairs. RESULTS: A modification of the weight
function used in the original version of the alignment program DIALIGN has
two important advantages: it can be applied to both globally and locally
related sequence sets, and the running time of the program is considerably
improved. The time complexity of the algorithm is discussed theoretically,
and the program running time is reported for various test examples.
AVAILABILITY: The program is available on- line at the Bielefeld University
Bioinformatics Server (BiBiServ)
http://bibiserv.TechFak.Uni-Bielefeld.DE/dial ign/
ARTICLES
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
GSF - National Research Center for Environment and Health, Institute of Biomathematics and Biometry, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany. burkhard.morgenstern@rp-rorer.co.uk
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A. Reimann, N. Nurhayati, A. Backenkohler, and D. Ober Repeated Evolution of the Pyrrolizidine Alkaloid-Mediated Defense System in Separate Angiosperm Lineages PLANT CELL, October 1, 2004; 16(10): 2772 - 2784. [Abstract] [Full Text] [PDF]
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C. T. Hittinger, A. Rokas, and S. B. Carroll Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts PNAS, September 28, 2004; 101(39): 14144 - 14149. [Abstract] [Full Text] [PDF]
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J. Gonzalez, F. Casals, and A. Ruiz Duplicative and Conservative Transpositions of Larval serum protein 1 Genes in the Genus Drosophila Genetics, September 1, 2004; 168(1): 253 - 264. [Abstract] [Full Text] [PDF]
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L. Lavie, P. Medstrand, W. Schempp, E. Meese, and J. Mayer Human Endogenous Retrovirus Family HERV-K(HML-5): Status, Evolution, and Reconstruction of an Ancient Betaretrovirus in the Human Genome J. Virol., August 15, 2004; 78(16): 8788 - 8798. [Abstract] [Full Text] [PDF]
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A. C.E. Darling, B. Mau, F. R. Blattner, and N. T. Perna Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Genome Res., July 1, 2004; 14(7): 1394 - 1403. [Abstract] [Full Text] [PDF]
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B. Morgenstern DIALIGN: multiple DNA and protein sequence alignment at BiBiServ Nucleic Acids Res., July 1, 2004; 32(suppl_2): W33 - W36. [Abstract] [Full Text] [PDF]
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M. Brudno, R. Steinkamp, and B. Morgenstern The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences Nucleic Acids Res., July 1, 2004; 32(suppl_2): W41 - W44. [Abstract] [Full Text] [PDF]
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L. Rohmer, D. S. Guttman, and J. L. Dangl Diverse Evolutionary Mechanisms Shape the Type III Effector Virulence Factor Repertoire in the Plant Pathogen Pseudomonas syringae Genetics, July 1, 2004; 167(3): 1341 - 1360. [Abstract] [Full Text] [PDF]
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L. Taher, O. Rinner, S. Garg, A. Sczyrba, and B. Morgenstern AGenDA: gene prediction by cross-species sequence comparison Nucleic Acids Res., July 1, 2004; 32(suppl_2): W305 - W308. [Abstract] [Full Text] [PDF]
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M. Stanke, R. Steinkamp, S. Waack, and B. Morgenstern AUGUSTUS: a web server for gene finding in eukaryotes Nucleic Acids Res., July 1, 2004; 32(suppl_2): W309 - W312. [Abstract] [Full Text] [PDF]
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 M. L. Pendrak, S. S. Yan, and D. D. Roberts Hemoglobin Regulates Expression of an Activator of Mating-Type Locus {alpha} Genes in Candida albicans Eukaryot. Cell, June 1, 2004; 3(3): 764 - 775. [Abstract] [Full Text] [PDF]
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L. M. Blayney, S. Zissimopoulos, E. Ralph, E. Abbot, L. Matthews, and F. A. Lai Ryanodine Receptor Oligomeric Interaction: IDENTIFICATION OF A PUTATIVE BINDING REGION J. Biol. Chem., April 9, 2004; 279(15): 14639 - 14648. [Abstract] [Full Text] [PDF]
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M. Blanchette, W. J. Kent, C. Riemer, L. Elnitski, A. F.A. Smit, K. M. Roskin, R. Baertsch, K. Rosenbloom, H. Clawson, E. D. Green, et al. Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner Genome Res., April 1, 2004; 14(4): 708 - 715. [Abstract] [Full Text] [PDF]
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M. Paumann, B. Lubura, G. Regelsberger, M. Feichtinger, G. Kollensberger, C. Jakopitsch, P. G. Furtmuller, G. A. Peschek, and C. Obinger Soluble CuA Domain of Cyanobacterial Cytochrome c Oxidase J. Biol. Chem., March 12, 2004; 279(11): 10293 - 10303. [Abstract] [Full Text] [PDF]
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 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]
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