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This paper explores two techniques for on-line exact pattern matching in files that have been compressed using the Burrows-Wheeler transform. We investigate two approaches. The first is an application of the Boyer-Moore algorithm (Boyer & Moore 1977) to a transformed string. The second approach is based on the observation that the transform effectively(More)
At the 3' end of all retroviral genomes there is a short, highly conserved sequence known as the polypurine tract (PPT), which serves as the primer for plus-strand DNA synthesis. We have identified the determinants for in vitro priming by the human immunodeficiency virus type 1 (HIV-1) PPT. We show that when the PPT is removed and placed into different(More)
We investigate off-line dictionary oriented approaches to DNA sequence compression, based on the Burrows-Wheeler Transform (BWT). The preponderance of short repeating patterns is an important phenomenon in biological sequences. Here, we propose off-line methods to compress DNA sequences that exploit the different repetition structures inherent in such(More)
In order to investigate how primer grip residues of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) contribute toward the architecture of its palm subdomain and neighboring structural elements, the DNA polymerase and ribonuclease H (RNase H) activities of enzymes bearing aromatic substitutions at Trp229 and Tyr232 of the(More)
Alanine-scanning mutants of the primer grip region of human immunodeficiency virus type 1 reverse transcriptase were tested for their ability to extend RNA and DNA versions of the polypurine tract primer, and an oligonucleotide representing the 18-nucleotide sequence at the 3' end of tRNALys3. A majority of the mutant enzymes were either completely or(More)
Between 1 January and 31 March 1991, 20 laboratories in England and Scotland sent a total of 413 consecutive clinical isolates of Moraxella catarrhalis to The London Hospital Medical College (LHMC). After confirmation of identity, the susceptibility of all isolates to 11 antimicrobial agents was determined. Of the 375 (90.8%) isolates which were found at(More)
Four hundred and thirty-one Streptococcus pneumoniae, 1272 Haemophilus influenzae and 305 Moraxella (Branhamella) catarrhalis were isolated from sputa and identified in 28 UK laboratories during a ten week period in 1990. Disc diffusion susceptibility testing was performed in each centre using identical methods. Species-specific susceptibility breakpoints(More)
The mechanisms of resistance to trimethoprim in eleven U.K. clinical isolates of Haemophilus influenzae were studied. The levels of dihydrofolate reductase (DHFR) activities in crude extracts from four resistant wild-types were similar to those in susceptible controls. However, activities in extracts from the other seven resistant wild-type isolates, and(More)
Two hundred and fifty-seven ampicillin-resistant clinical isolates of Haemophilus influenzae were tested by disk diffusion and MIC determination for susceptibility to aztreonam, imipenem, and amoxycillin combined with clavulanate. The modal MICs and MICs for 50 and 90% of isolates of all three antimicrobial agents for the 157 beta-lactamase-positive strains(More)