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Title: Alignments of sequences with repeats
P173
Wagner, Holger

hwagner@mathematik.uni-bielefeld.de
CeBiTec, Universität Bielefeld, Postfach 100131, 33594 Bielefeld, Germany

Let us consider the alignment of 2 Sequences A and B, where A is the concatenation of two substrings a and a' and where a, a' and B are similar strings. Then there are two pairwise alignments of A and B with nearly the same score values:

a a' and a a'
B B

Correspondingly, multiple sequences alignments of strings with the structure of A or B resp. have a score function with many local maxima of nearly the same height. On the other hand, the corresponding alignments often lead to completely different interpretation by tools for phylogenetic analysis. For example, the alignments

a a' and a a'
B B
C C

will result in different distances (or similarities) between B and C. Thus, it is necessary to not only consider the global maxima of such multiple sequence alignments, but also local maxima and to derive additional criteria to evaluate these alignments.

These analyses are performed for aminoacid sequences of bacterial ABC-transporters (ATP-Binding cassette-transporters) - a class of permeases. Particularly, two new options of the alignment program dialign [1] are very helpful for these analyses.
[1] B. Morgenstern, A. Dress, and T. Werner: Multiple DNA and protein sequence alignments based on segment-to-segment comparison, Proc. Natl. Acad. Sci. USA 93 (1996), 12098-12103.