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Andreas Dress

Publications and source records attributed to Andreas Dress.

6 recordsLinked to original sources
PubMed2006

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets.

We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network. To illustrate the applicability of QNet, we apply it to a previously published Salmonella data set. We conclude that QNet can provide a useful alternative to NNet if distance data are not available or a character-based approach is preferred. Moreover, it can be used as an aid for determining when a quartet-based tree-building method may or may not be appropriate for a given data set. QNet is freely available for download.

Algorithms↗
PubMed2004

Comparative homology agreement search: an effective combination of homology-search methods.

Many methods have been developed to search for homologous members of a protein family in databases, and the reliability of results and conclusions may be compromised if only one method is used, neglecting the others. Here we introduce a general scheme for combining such methods. Based on this scheme, we implemented a tool called comparative homology agreement search (chase) that integrates different search strategies to obtain a combined "E value." Our results show that a consensus method integrating distinct strategies easily outperforms any of its component algorithms. More specifically, an evaluation based on the Structural Classification of Proteins database reveals that, on average, a coverage of 47% can be obtained in searches for distantly related homologues (i.e., members of the same superfamily but not the same family, which is a very difficult task), accepting only 10 false positives, whereas the individual methods obtain a coverage of 28-38%.

Databases, Protein↗
PubMed2003

AltAVisT: comparing alternative multiple sequence alignments.

UNLABELLED: We introduce a WWW-based tool that is able to compare two alternative multiple alignments of a given sequence set. Regions where both alignments coincide are color-coded to visualize the local agreement between the two alignments and to identify those regions that can be considered to be reliably aligned. AVAILABILITY: http://bibiserv.techfak.uni-bielefeld.de/altavist/.

Color↗
PubMed2003

From sphere to torus: a topological view of the metazoan body plan.

From the viewpoint of mathematical topology, membrane systems in intact living cells can be described as closed and orientable surfaces, i.e., as surfaces with two sides and no boundary lines so that an 'inside' and an 'outside' can be distinguished. Usually, biomembranes represent topological spheres, often one embedded in another one. Toroidal membranes are occasionally observed, e.g., in specialized structures of plant cells like the prolamellar body. Here, we propose that rules analogous to those that govern the topology of biomembranes hold for the epithelial cell sheets that cover anatomically external as well as internal surfaces of multicellular animals. We suggest to study the emergence of morphological complexity during metazoan development using concepts from mathematical topology, and propose experimental analyses of those topological transitions that appear to be relevant in development and evolution.

Animals↗