Short report

Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family

Holger Wagner¹ , Burkhard Morgenstern² and Andreas Dress^3,4

¹  FSPM, Faculty of Mathematics, Bielefeld University, Postfach 100131, D-33501 Bielefeld, Germany

²  Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, Germany

³  CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031 Shanghai, PR China

⁴  Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22 – 26, D-04103 Leipzig, Germany

author email corresponding author email

Algorithms for Molecular Biology 2008, 3:15doi:10.1186/1748-7188-3-15

Published:	6 November 2008

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.