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
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
Autor
; ;
Abstract / Bemerkung
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.
Erscheinungsjahr
Zeitschriftentitel
Algorithms for Molecular Biology
Band
3
Ausgabe
1
Seite(n)
15
ISSN
PUB-ID

Zitieren

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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
1970-01-01T00:00:00Z

2 Zitationen in Europe PMC

Daten bereitgestellt von 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
A min-cut algorithm for the consistency problem in multiple sequence alignment.
Corel E, Pitschi F, Morgenstern B., Bioinformatics 26(8), 2010
PMID: 20189940

36 References

Daten bereitgestellt von Europe PubMed Central.

A canonical decomposition theory for metrics on a finite set
Bandelt H-J, Dress A., 1992
The composite genome of the legume symbiont Sinorhizobium meliloti.
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J., Science 293(5530), 2001
PMID: 11474104
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.
Brudno M, Steinkamp R, Morgenstern B., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215346
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid.
Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481432

Durbin R, Eddy SR, Krogh A, Mitchison G., 1998
Phylogenies from molecular sequences: inference and reliability.
Felsenstein J., Annu. Rev. Genet. 22(), 1988
PMID: 3071258

Felsenstein J., 2003
Detection of internal repeats: how common are they?
Heringa J., Curr. Opin. Struct. Biol. 8(3), 1998
PMID: 9666330
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
Katoh K, Kuma K, Toh H, Miyata T., Nucleic Acids Res. 33(2), 2005
PMID: 15661851
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
Quality assessment of multiple alignment programs.
Lassmann T, Sonnhammer EL., FEBS Lett. 529(1), 2002
PMID: 12354624
An exact solution for the segment-to-segment multiple sequence alignment problem.
Lenhof HP, Morgenstern B, Reinert K., Bioinformatics 15(3), 1999
PMID: 10222407
The Escherichia coli ATP-binding cassette (ABC) proteins.
Linton KJ, Higgins CF., Mol. Microbiol. 28(1), 1998
PMID: 9593292
Prediction of target substrates of transporters in escherichia coli
Matsusaki S, Watanabe H, Oshima T, Kanaya S, Mori H., 2002
A space-efficient algorithm for aligning large genomic sequences.
Morgenstern B., Bioinformatics 16(10), 2000
PMID: 11120687
A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
Morgenstern B., 2002
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.
Morgenstern B., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215344
Multiple DNA and protein sequence alignment based on segment-to-segment comparison.
Morgenstern B, Dress A, Werner T., Proc. Natl. Acad. Sci. U.S.A. 93(22), 1996
PMID: 8901539
AltAVisT: comparing alternative multiple sequence alignments.
Morgenstern B, Goel S, Sczyrba A, Dress A., Bioinformatics 19(3), 2003
PMID: 12584133
Multiple sequence alignment with user-defined anchor points.
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), 2004
PMID: 15546937
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
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
Phylogeny reconstruction
Swofford D, Olsen G., 1990
A comprehensive comparison of multiple sequence alignment programs.
Thompson JD, Plewniak F, Poch O., Nucleic Acids Res. 27(13), 1999
PMID: 10373585

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 18990223
PubMed | Europe PMC

Suchen in

Google Scholar