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BACKGROUND We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by(More)
In this paper, we present boundary labeling, a new approach for labeling point sets with large labels. We first place disjoint labels around an axis-parallel rectangle that contains the points. Then we connect each label to its point such that no two connections intersect. Such an approach is common e.g. in technical drawings and medical atlases, but so far(More)
The existing literature gives efficient algorithms for mapping trees or less restrictively outerplanar graphs on a given set of points in a plane, so that the edges are drawn planar and as straight lines. We relax the latter requirement and allow very few bends on each edge while considering general plane graphs. Our results show two algorithms for mapping(More)
Sugiyama's algorithm for layered graph drawing is very popular and commonly used in practical software. The extensive use of dummy vertices to break long edges between non-adjacent layers often leads to unsatis-fying performance. The worst-case running-time of Sugiyama's approach is O(|V ||E| log |E|) requiring O(|V ||E|) memory, which makes it unusable for(More)
Two trees with the same number of leaves have to be embedded in two layers in the plane such that the leaves are aligned in two adjacent layers. Additional matching edges between the leaves give a one-to-one correspondence between pairs of leaves of the different trees. Do there exist two planar embeddings of the two trees that minimize the crossings of the(More)
BACKGROUND DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy(More)
BACKGROUND High-throughput methods that allow for measuring the expression of thousands of genes or proteins simultaneously have opened new avenues for studying biochemical processes. While the noisiness of the data necessitates an extensive pre-processing of the raw data, the high dimensionality requires effective statistical analysis methods that(More)
A major factor affecting the readability of an illustration that contains textual labels is the degree to which the labels obscure graphi-cal features of the illustration as a result of spatial overlaps. Boundary labeling addresses this problem by attaching the labels to the boundary of a rectangle that contains all features. Then, each feature should be(More)
We consider the problem of drawing a set of simple paths along the edges of an embedded underlying graph G = (V, E), so that the total number of crossings among pairs of paths is minimized. This problem arises when drawing metro maps, where the embedding of G depicts the structure of the underlying network, the nodes of G correspond to train stations, an(More)