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The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate(More)
The specificity of serological tests for Lyme borreliosis is impaired by cross-reacting antibodies. In order to select antigens for more specific tests, specific and cross-reactive proteins of Borrelia burgdorferi must be identified. Therefore, to analyze cross reactions of Borrelia burgdorferi with other bacteria, rabbit immune sera against heterologous(More)
MOTIVATION Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. RESULTS We describe a(More)
A tool is presented that helps to find biological functions for new protein sequences. Running on any Macintosh computer system, MacPattern provides a unique combination of different algorithms, speed and user-friendliness. It supports searches for protein patterns using the PROSITE database, protein block searches with the BLOCKS database, and the(More)
A new program, BlockSearch, is described that allows biologists to search protein sequences against the BLOCKS database of aligned protein blocks by converting these blocks to site-specific scoring matrices. It thus complements existing tools for standard similarity searches and pattern searches which aid in elucidating the function of newly determined(More)
Profile searches using aligned short protein blocks are an effective method for identifying putative protein functions. An algorithm is presented that accelerates block searches by a factor 2-5 with only limited lack of sensitivity; this algorithm is particularly suited for application in large-scale genome research.
The 8p11 myeloproliferative syndrome (EMS) also known as stem cell leukemia-lymphoma syndrome (SCLL) is associated with translocations that disrupt FGFR1. The resultant fusion proteins are constitutively active tyrosine kinases, and different FGFR1 fusions are associated with subtly different disease phenotypes. We report here a patient with a(More)
We describe the cloning and expression of the pc gene which encodes a major immunodominant protein of Borrelia burgdorferi, the causative agent of Lyme borreliosis. The pC protein was purified from lysates of B. burgdorferi strain PKo. After tryptic digestion of the pC protein the resulting oligopeptides were applied to a gas-phase sequenator. Thus partial(More)
Cardiac hypertrophy and heart failure are frequently accompanied by elevated plasma levels of tumor necrosis factor alpha (TNF alpha), the pathogenetic relevance of this finding being a matter of debate. In human acute septic cardiomyopathy, on the other hand, the negative inotropic impact of TNF alpha on the heart is well documented and frequently ascribed(More)