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Vincens P; Buffat L; Andre C; Chevrolat JP; Boisvieux JF; Hazout S 《Bioinformatics (Oxford, England)》1998,14(8):715-725
MOTIVATION: Complete genomic sequences will become available in the future.
New methods to deal with very large sequences (sizes beyond 100 kb)
efficiently are required. One of the main aims of such work is to increase
our understanding of genome organization and evolution. This requires
studies of the locations of regions of similarity. RESULTS: We present here
a new tool, ASSIRC ('Accelerated Search for SImilarity Regions in
Chromosomes'), for finding regions of similarity in genomic sequences. The
method involves three steps: (i) identification of short exact chains of
fixed size, called 'seeds', common to both sequences, using hashing
functions; (ii) extension of these seeds into putative regions of
similarity by a 'random walk' procedure; (iii) final selection of regions
of similarity by assessing alignments of the putative sequences. We used
simulations to estimate the proportion of regions of similarity not
detected for particular region sizes, base identity proportions and seed
sizes. This approach can be tailored to the user's specifications. We
looked for regions of similarity between two yeast chromosomes (V and IX).
The efficiency of the approach was compared to those of conventional
programs BLAST and FASTA, by assessing CPU time required and the regions of
similarity found for the same data set. AVAILABILITY: Source programs are
freely available at the following address: ftp://ftp.biologie.ens.
fr/pub/molbio/assirc.tar.gz CONTACT: vincens@biologie.ens.fr,
hazout@urbb.jussieu.fr
相似文献
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James?F?MeschiaEmail author Thomas?G?Brott Robert?D?BrownJr Richard?JP?Crook Michael?Frankel John?Hardy José?G?Merino Stephen?S?Rich Scott?Silliman Bradford?Burke?Worrall 《BMC neurology》2003,3(1):4
Background
The molecular basis for the genetic risk of ischemic stroke is likely to be multigenic and influenced by environmental factors. Several small case-control studies have suggested associations between ischemic stroke and polymorphisms of genes that code for coagulation cascade proteins and platelet receptors. Our aim is to investigate potential associations between hemostatic gene polymorphisms and ischemic stroke, with particular emphasis on detailed characterization of the phenotype. 相似文献76.
S. Troupel G. Le Moel A. Bouten H. Fessi Z. Boukhalfa G. Stamatakis V. Lecon JP. Mery J. Agneray C. Jacobs 《Amino acids》1992,2(1-2):127-132
Summary A well preserved nutritional status is beneficial in chronically uremic patients for slowing the pace of deterioration of renal function, and delaying the need for dialysis therapy. The purpose of this study was to assess the nutritional profile of 10 patients in a steady state of advanced CRF, and of 15 patients with terminal renal failure immediately prior to their first hemodialysis session (J0), and 7, 14, 45, 60, days post start of dialysis. Patients were 18 to 65 years old with total plasma proteins 60g/1. Plasma concentrations of amino acids, nutrition proteins, apolipoproteins A1, and B were evaluated. Non inflammatory reaction was evaluated by determination of alpha-1-acid glycoprotein, and C reactive protein. The data (mean ± 1 SD) were compared with mean values of 15 healthy individuals. 相似文献
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Luis Clepf Passos Marianne Araújo Soares Mariana Abreu Costa JP Michaud Brenda Carolina Freire Geraldo Andrade Carvalho 《Biocontrol Science and Technology》2017,27(9):1082-1095
In order to aid the integration of biological and chemical controls for the tomato leaf miner, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), this study evaluated the relative toxicity of five insecticides to the leaf miner predator Macrolophus basicornis (Stal) (Hemiptera: Miridae). The insecticides evaluated were teflubenzuron, abamectin, chlorantraniliprole, chlorfenapyr, and cartap hydrochloride, all of which are recommended for control of T. absoluta in Brazil. Nymphs and adults of M. basicornis were exposed to tomato leaves treated with the insecticides, under laboratory and greenhouse conditions. The overall mortality caused by the products in both situations was recorded, and the survival of congeneric groups was analysed using the Weibull model. The persistence of the insecticides was also evaluated and they were categorised into toxicity classes proposed by the International Organisation for Biological Control (IOBC) based on predator mortality and persistence. Abamectin and chlorfenapyr were toxic to M. basicornis nymphs and adults in all bioassays. Cartap hydrochloride was slightly harmful to adults in laboratory assays, but harmful to nymphs, and moderately harmful under greenhouse conditions. Chlorantraniliprole and teflubenzuron were harmless in most assays, except when nymphs were exposed in the laboratory, where they were moderately and slightly harmful, respectively. Chlorantraniliprole and teflubenzuron should be preferred insecticides for use in tomato leaf miner IPM programmes that aim to conserve M. basicornis populations. 相似文献
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