Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family
Wagner H, Morgenstern B, Dress A (2008)
Algorithms for Molecular Biology 3(1): 15.
Download
Journal Article
| Published
| English
Author
Wagner, Holger
;
Morgenstern, Burkhard
;
Dress, Andreas
Department
Abstract
Background: Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlying alignments is therefore crucial for phylogenetic analysis. Results: In this short report, we investigate alignments and alignment-based phylogenies constructed for a set of 22 ABC transporters using CLUSTAL W and DIALIGN. Comparing the 22 "one-out phylogenies" one can obtain for this sequence set, some intrinsic phylogenetic instability is observed - even if attention is restricted to branches with high bootstrapping frequencies, the so-called safe branches. We show that this instability is caused by the fact that both, CLUSTAL W as well as DIALIGN, apparently get "confused" by sequence repeats in some of the ABC-transporter. To deal with such problems, two new DIALIGN options are introduced that prove helpful in our context, the "exclude-fragment" (or "xfr") and the "self-comparison" (or "sc") option. Conclusion: "One-out strategies", known to be a useful tool for testing the stability of all sorts of data-analysis procedures, can successfully be used also in testing alignment stability. In case instabilities are observed, the sequences under consideration should be carefully checked for putative causes. In case one suspects sequence repeats to be the cause, the new "sc" option can be used to detect such repeats, and the "xfr" option can help to resolve the resulting problems.
Publishing Year
ISSN
PUB-ID
Cite this
Wagner H, Morgenstern B, Dress A. Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms for Molecular Biology. 2008;3(1):15.
Wagner, H., Morgenstern, B., & Dress, A. (2008). Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms for Molecular Biology, 3(1), 15. doi:10.1186/1748-7188-3-15
Wagner, H., Morgenstern, B., and Dress, A. (2008). Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms for Molecular Biology 3, 15.
Wagner, H., Morgenstern, B., & Dress, A., 2008. Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms for Molecular Biology, 3(1), p 15.
H. Wagner, B. Morgenstern, and A. Dress, “Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family”, Algorithms for Molecular Biology, vol. 3, 2008, pp. 15.
Wagner, H., Morgenstern, B., Dress, A.: Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms for Molecular Biology. 3, 15 (2008).
Wagner, Holger, Morgenstern, Burkhard, and Dress, Andreas. “Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family”. Algorithms for Molecular Biology 3.1 (2008): 15.
All files available under the following license(s):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Main File(s)
File Name
Access Level

This data publication is cited in the following publications:
This publication cites the following data publications:
2 Citations in Europe PMC
Data provided by Europe PubMed Central.
Identification and Characterization of microRNA319a and Its Putative Target Gene, PvPCF5, in the Bioenergy Grass Switchgrass (Panicum virgatum).
Xie Q, Liu X, Zhang Y, Tang J, Yin D, Fan B, Zhu L, Han L, Song G, Li D., Front Plant Sci 8(), 2017
PMID: 28424710
Xie Q, Liu X, Zhang Y, Tang J, Yin D, Fan B, Zhu L, Han L, Song G, Li D., Front Plant Sci 8(), 2017
PMID: 28424710
A min-cut algorithm for the consistency problem in multiple sequence alignment.
Corel E, Pitschi F, Morgenstern B., Bioinformatics 26(8), 2010
PMID: 20189940
Corel E, Pitschi F, Morgenstern B., Bioinformatics 26(8), 2010
PMID: 20189940
36 References
Data provided by Europe PubMed Central.
Multiple sequence alignment with user-defined anchor points.
Morgenstern B, Prohaska SJ, Pohler D, Stadler PF., Algorithms Mol Biol 1(1), 2006
PMID: 16722533
Morgenstern B, Prohaska SJ, Pohler D, Stadler PF., Algorithms Mol Biol 1(1), 2006
PMID: 16722533
Multiple sequence alignment with user-defined constraints at GOBICS.
Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J., Bioinformatics 21(7), 2005
PMID: 15546937
Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J., Bioinformatics 21(7), 2005
PMID: 15546937
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
Needleman SB, Wunsch CD., J. Mol. Biol. 48(3), 1970
PMID: 5420325
Needleman SB, Wunsch CD., J. Mol. Biol. 48(3), 1970
PMID: 5420325
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou N, Nei M., Mol. Biol. Evol. 4(4), 1987
PMID: 3447015
Saitou N, Nei M., Mol. Biol. Evol. 4(4), 1987
PMID: 3447015
Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.
Saurin W, Hofnung M, Dassa E., J. Mol. Evol. 48(1), 1999
PMID: 9873074
Saurin W, Hofnung M, Dassa E., J. Mol. Evol. 48(1), 1999
PMID: 9873074
ATP-binding-cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains.
Schneider E, Hunke S., FEMS Microbiol. Rev. 22(1), 1998
PMID: 9640644
Schneider E, Hunke S., FEMS Microbiol. Rev. 22(1), 1998
PMID: 9640644
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.
Subramanian AR, Kaufmann M, Morgenstern B., Algorithms Mol Biol 3(), 2008
PMID: 18505568
Subramanian AR, Kaufmann M, Morgenstern B., Algorithms Mol Biol 3(), 2008
PMID: 18505568
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.
Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B., BMC Bioinformatics 6(), 2005
PMID: 15784139
Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B., BMC Bioinformatics 6(), 2005
PMID: 15784139
Phylogeny reconstruction
Swofford D, Olsen G., 1990
Swofford D, Olsen G., 1990
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ., Nucleic Acids Res. 22(22), 1994
PMID: 7984417
Thompson JD, Higgins DG, Gibson TJ., Nucleic Acids Res. 22(22), 1994
PMID: 7984417
A comprehensive comparison of multiple sequence alignment programs.
Thompson JD, Plewniak F, Poch O., Nucleic Acids Res. 27(13), 1999
PMID: 10373585
Thompson JD, Plewniak F, Poch O., Nucleic Acids Res. 27(13), 1999
PMID: 10373585
Export
0 Marked PublicationsWeb of Science
View record in Web of Science®Sources
PMID: 18990223
PubMed | Europe PMC