A new type of search algorithm to find biological information inherited in nucleic acid sequences was developed. The algorithm is of pattern match type and is based on the fact that genetic information often is a function of a predictable statistical occurrence of the four bases within parts of the sequence. The search algorithm compares the known statistical pattern of bases in e.g. a promoter, with an unknown sequence and calculates the statistical significance of the match at all positions in the unknown sequence. The program was tested on 54 published prokaryotic promoters. 44 or 49 could be found with 1 or 4 false answers, respectively. The program was also used on plasmid pBR322. All promoters functioning in an in vitro transcription system were found (tet, anti-tet, p4, bla and ori) except the so called p5 promoter. A search for donor and acceptor sites was performed in a human HLA genomic sequence that contains six introns. Five of the possible six donor and acceptor sites were found.
We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+
We describe a computer program designed to facilitate the pattern matching analysis of homologies between DNA sequences. It takes advantage of a two-dimensional plot in order to simplify the evaluation of significant structures inherited in the sequences. The program can be divided into three parts, i) algorithm for search of homologies, ii) two-dimensional graphic display of the result, iii) further graphic treatment to enhance significant structures. The power of the graphic display is presented by the following application of the program. We conducted a search for direct repeats in the mouse immunoglobulin kappa-chain genes. Both the five J DNA sequences and other shorter repeats were found. We also found a longer stretch of homology that could indicate the presence of duplicated DNA in the J4, J5 region.
A cosmid gene library of Actinomyces viscosus T14V was prepared in Escherichia coli to examine the expression ofA. viscosus antigens and to gain insight idto the structure ofA. viscosus type 1 and type 2 fimbriae. Out of this library of 550 clones, 28 reacted in a colony immunoassay with antibodies against A. viscosus cells. The proteins responsible for these reactions were identified in three clones. Clones AV1209 and AV2009 displayed nonfimbrial antigens with subunits of 40 and 58 kilodaltons, respectively. Clone AV1402 showed a 59-kilodalton protein that reacted with monospecific antibody against type 2 fimbriae and that comigrated with a subunit of type 2 fimbriae during sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This indicates that AV1402 expresses a gene (fimA) for a subunit of A. viscosus type 2 fimbriae.Actinomyces viscosus is a gram-positive bacterium that is often found in high numbers in human dental plaque, where it may play a role in periodontal infections (reviewed in reference 14). The colonization of teeth by this microbe involves two antigenically distinct types of fimbriae (type 1 and type 2). Type 1 fimbriae selectively promote adherence to saliva-coated hydroxyapatite (9, 28). In contrast, type 2 fimbriae mediate attachment of A. -viscosus to certain streptococci that predominate in developing dental plaque (7). This latter property depends on a lactose-sensitive lectin activity associated with type 2 fimbriae (6, 8, 25) and complementary carbohydrate-containing receptors on the streptococcal surface. Whereas the existence and function of each type of fimbriae has been clearly demonstrated, little is known about their subunits. This is largely due to their resistance to dissociation by methods that will extensively depolymerize fimbriae from gram-negative organisms (23,28). To identify and characterize putative subunits and precursors of A. viscosus fimbriae, a study to clone the respective genes was undertaken.MATERIALS AND METHODS Strains. Escherichia coli HB101 (3) and A. viscosus T14V (6, 8) have been described previously.Preparation of A. viscosus T14V chromosomal DNA. Cells were grown in 400 ml of medium and treated with lysozyme as described (5). They were suspended in 40 ml of 10 mM Tris-1 mM EDTA (pH 8.0), and lysed by adding 4.4 ml of 10% sodium dodecyl sulfate (SDS) with a 15-min incubation at 65°C. In this and subsequent steps care was taken not to shear the DNA. The viscous lysate was extracted with an equal volume of phenol saturated with 3% NaCl and then with chloroforn-isoamyl alcohol (24:1 [vol/vol]). After addition of 2 volumes of ethanol, the precipitate was collected by centrifugation and dissolved in 25 ml of 10 mM Tris-1 mM EDTA-10 mM NaCl (pH 8.0). After treatment with RNase A (100 p.g/ml) and RNase Ti (100 U/ml) for 1 h at 37°C, proteinase K was added (100 ,ug/ml), and the incubation was continued at 55°C for another hour. The solution was extracted with phenol and chloroform as described previously, adjusted to 3 M ammonium acetate, and left at 4°C for ...
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