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Dose-dependent regulation of the early promoter of human papillomavirus type 18 by the viral E2 protein.
The activity of the E6/E7 promoter of genital human papillomaviruses (HPVs) is positively and negatively modulated by a complex interplay between a variety of cellular transcription factors and theExpand
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An enhanced RNA alignment benchmark for sequence alignment programs
TLDR
We enhance the first RNA alignment benchmark published so far and show that sequence alignment programs perform equally well on RNA sequence sets with high sequence identity, that is with an average pairwise sequence identity. Expand
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Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction.
  • G. Steger
  • Mathematics, Medicine
  • Nucleic acids research
  • 25 July 1994
A program is described which calculates the thermal stability and the denaturation behaviour of double-stranded DNAs and RNAs up to a length of 1000 base pairs. The algorithm is based on recursiveExpand
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RNA structural features responsible for potato spindle tuber viroid pathogenicity.
The native structure of potato spindle tuber viroid (PSTVd) contains a series of short double helices and small internal loops that are organized into five structural domains. Nucleotides within theExpand
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StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
TLDR
We present StrAl, a heuristic method for alignment of ncRNA that reduces sequence-structure alignment to a two-dimensional problem similar to standard sequence alignment. Expand
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Effects of random mutagenesis upon potato spindle tuber viroid replication and symptom expression.
A combination of random chemical mutagenesis plus temperature gradient gel electrophoresis was used to isolate a collection of 57 potato spindle tuber viroid (PSTV) cDNAs containing mutationsExpand
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The hepatitis B virus post-transcriptional regulatory element contains two conserved RNA stem-loops which are required for function.
Human Hepatitis B Virus (HBV) RNAs contain a cis -acting sequence, the post-transcriptional regulatory element (HPRE), which facilitates the cytoplasmic localization of intronless transcripts. OurExpand
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Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data.
Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroidsExpand
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NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome
MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their regulatory activity is mediatedExpand
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Biolistic inoculation of plants with viroid nucleic acids.
Parameters for biolistic transfer of viroid nucleic acids using a Helios Gene Gun device were assayed. The main achievement of this method is high efficiency of inoculation with linear monomericExpand
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