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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 p100 gene coding for the p100 protein of Borrelia burgdorferi strain PKo has been cloned, sequenced and expressed in Escherichia coli. An open reading frame including upstream and downstream sequences with potential translation and transcription signals could be identified. The reading frame consists of 1989 nucleotides corresponding to a protein of 663(More)
The genes coding for the outer surface protein (OspA) of Borrelia burgdorferi, the causative agent of Lyme borreliosis have been cloned and sequenced. Two German strains (skin isolate PKo and cerebrospinal fluid isolate PBi) have been analyzed. Using an OspA-specific monoclonal antibody (L32 2E7) for immunological screening of a genomic pUC 18 library of B.(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 ofBorrelia burgdorferi must be identified. Therefore, to analyze cross reactions ofBorrelia burgdorferi with other bacteria, rabbit immune sera against heterologous(More)
The ospC gene coding for the outer surface protein OspC and the fla gene coding for the flagellin have been investigated in three different Borrelia burgdorferi sensu lato strains. These strains (the North American strain B31 and the European strains PKo and PBi) derive from various biological sources (lxodes dammini, human skin and human CSF) and belong to(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.