BACKGROUND Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. RESULTS Giv...

Dislocation following total hip replacement surgery (THR) remains a significant clinical problem. Malposition of the acetabular component increases the occurrence of impingement, reduces the " safe " range of motion and increases the risk of dislocation. Not fully understanding the interaction between pelvic orientation and final acetabular cup alignment may be one of the main contributing fact...

Sequence alignment visualization is an important tool for understanding genomics data. Current approaches have difficulty scaling to the larger data sets becoming available. In this work, we survey recent results from perceptual science and show how they provide ideas for creating more scalable alignment visualization tools. We identify several principles, discuss how they inform alignment visu...

Two online research tools are presented in this paper: PermA, a general-purpose string aligner which can for example be used for grapheme-to-phoneme and phonemeto-phoneme alignment, and Balloon, a text processing toolkit for German and English providing components for part-of-speech tagging, morphological analyses, and grapheme-to-phoneme conversion including syllabification and word-stress ass...

SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences a...

Multiple structural alignment is a fundamental problem in structural genomics. In this article, we define a reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the C(alpha) atoms in the set. Broadly based ...

MOTIVATION The combination of liquid chromatography and mass spectrometry (LC/MS) has been widely used for large-scale comparative studies in systems biology, including proteomics, glycomics and metabolomics. In almost all experimental design, it is necessary to compare chromatograms across biological or technical replicates and across sample groups. Central to this is the peak alignment step, ...

Purpose – By providing interoperability users can be supported in sharing and reusing vocabularies and knowledge. Ontology alignment plays an important role in the context of semantic interoperability. Usually ontology alignment tools generate results that are difficult to understand or assess. In order to enable users to check and improve alignment results and to understand their consequences ...