RESUMO
This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse-based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mirror repeats (triplex DNA), direct/tandem repeats (slipped/hairpin structures), G4 motifs (tetraplex, G-quadruplex DNA), alternating purine-pyrimidine tracts (left-handed Z-DNA), and A-phased repeats (static bending). The nBMST is versatile, simple to use, does not require bioinformatics skills, and can be applied to any type of DNA sequences, including viral and bacterial genomes, up to an aggregate of 20 megabasepairs (Mbp).
Assuntos
Biologia Computacional/métodos , DNA/química , Ferramenta de Busca , Animais , Bases de Dados de Ácidos Nucleicos , Humanos , Internet , Conformação de Ácido Nucleico , Motivos de NucleotídeosRESUMO
A five-month-old, male Brazilian fila presented with a three-day history of a focal swelling in the left superior palpebra and a focal, subcutaneous swelling over the dorsal cervical region. Both lesions initially responded to warm compresses and a two-week course of oral amoxicillin-clavulanic acid therapy. The eyelid swelling recurred after discontinuation of the oral antibiotic therapy. The lesion was progressive and was refractory to trimethoprim-sulfadiazine therapy. Culture and sensitivity performed from a surgical biopsy sample of the eyelid mass identified Actinomyces viscosus and other bacterial genera. A combination of surgical debulkment, Penrose drain placement, and a one-month course of oral oxacillin therapy has resulted in clinical regression of the lesion at a six-month postoperative evaluation.
