Fluorescence in situ hybridization (FISH) resolution has advanced because newer techniques use increasingly decondensed chromatin. FISH cannot analyze restriction enzyme cutting sites due to limitations of the hybridization and detection technologies. The RecA-assisted restriction endonuclease (RARE) technique cleaves chromosomal DNA at a single EcoRI site within a given gene or selected sequen...

A method based on RT-PCR and restriction endonuclease digestion of amplified PCR product was used to differentiate rabies laboratory “fixed” and “street” viruses. The primer sets from glycoprotein and nucleoprotein gene of rabies virus were used to amplify 406 and 533 bp amplicons, respectively. After amplification in RT-PCR, the PCR product was digested with HaeIII restriction endonuclease and...

Nucleotide sequences of 16S rDNA and rpoB gene of 25 bovine and 6 ovine Histophilus somni strains were determined to detect subtle differences between the host animal species. The 1465 nucleotide residues of the 16S rDNA exhibited levels of sequence similarities of 99.4% or more. The high sequence similarity of the 16S rDNA of recently described species H. somni was confirmed in the 31 strains ...

The DNA of 48 strains of adenovirus type 40 (Ad40) and of 128 strains of adenovirus type 41 (Ad41), isolated between 1971 and 1986 from various countries, was characterized by restriction enzyme analysis using nine and ten restriction endonucleases respectively. Five new DNA variants of Ad40 and 18 new DNA variants of Ad41 were detected. Most of the restriction sites which differed among the va...

Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "in vi...

The genetic diversity of the human immunodeficiency virus (HIV) isolated from transfusion-associated AIDS patients has been examined. Restriction enzyme mapping studies of integrated proviral DNA of donor and recipient origin demonstrated genomic variation between isolates. Analysis of the molecularly cloned viral genomes of one donor-recipient pair showed that virus from the recipient had rest...

We present a new, practical algorithm to resolve the experimental data in restriction site analysis, which is a common technique for mapping DNA. Specifically, we assert that multiple digestions with a single restriction enzyme can provide sufficient information to identify the positions of the restriction sites with high probability. The motivation for the new approach comes from combinatorial...

Two algorithms are described that rapidly construct restriction maps of DNA molecules from single- and double-digest data. The implementation of these algorithms into the Pascal programs AMAPK and AMARD allows such mapping to be done on microcomputers.