Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide

Zuker, Michael; Mathews, David H.; Turner, Douglas H.

doi:10.1007/978-94-011-4485-8_2

Cited by 943 publications

(825 citation statements)

References 36 publications

Supporting

Mentioning

803

Contrasting

Unclassified

Order By: Relevance

“…Secondary structure of the pyr RNA specified by template 2 in the predicted PyrR-bound terminator (A) and antiterminator (B) conformations showing the location of transcription pause sites (P and bold arrows) and mutations (dashed arrows to base substitutions) characterized in this study. MFOLD version 3.1 (Zuker et al 1999) was used to predict these structures. The nucleotide sequences are numbered from the start of transcription of the pyr operon as +1.…”

Section: Discussionmentioning

confidence: 99%

“…1). The free energies of formation of the wild type antiterminator stem-loop were calculated with MFOLD version 3.1 (Zuker et al 1999) as −24.2 kcal/mol and for the U781G and U781A mutants as −24.1 kcal/mol and −25.2 kcal/mol , respectively.…”

Section: Mutation Of Pyr Dna Templates At the Site Of The 3' Terminusmentioning

confidence: 99%

“…1). Analysis with the MFOLD computer program (Zuker et al 1999) indicated that the C791A mutation reduces the stability of the terminator hairpin by about 5 kcal/mol, which is almost 40% of its calculated free energy of formation. None of the other mutations studied in this work were predicted to alter the free energy of formation of secondary structures significantly.…”

Section: Expression and Regulation In Vivo Of Pyr-lacz Fusions Contaimentioning

confidence: 99%

See 2 more Smart Citations

Mutations affecting transcription pausing in the Bacillus subtilis pyr operon

2005

View full text Add to dashboard Cite

Pausing during transcription of the Bacillus subtilis pyr operon has been proposed to play a role in its regulation by attenuation. Substitution mutations in the B. subtilis pyr DNA specifying the 3'-terminal nucleotides of previously identified transcription pause sites substantially reduced pausing at these sites in vitro. This result confirms the general utility of this mutagenic strategy for studying transcriptional pausing. Pyrimidine-mediated repression in vivo of pyr-lacZ fusions containing some of these substitution mutations was substantially lower than observed with the wild-type pyr-lacZ fusions. However, these defects in regulation were correlated with alterations in the stability of the terminator stem-loop specified by the attenuator, rather than with their effects on transcriptional pausing in vitro.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Mutation Of Pyr Dna Templates At the Site Of The 3' Terminusmentioning

confidence: 99%

Section: Expression and Regulation In Vivo Of Pyr-lacz Fusions Contaimentioning

confidence: 99%

See 1 more Smart Citation

Mutations affecting transcription pausing in the Bacillus subtilis pyr operon

2005

View full text Add to dashboard Cite

show abstract

“…The Vienna RNA package can be used to predict secondary structures in either a Unix or Windows environment and is covered in unit 12.2 (Hofacker et al, 1994). The use of the mfold web server for secondary structure prediction is covered in Current Protocols in Nucleic Acid Chemistry in unit 11.2 (Zuker et al, 1999). The commentary at the end of the unit compares the available packages.…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

RNA Secondary Structure Analysis Using RNAstructure

Mathews

2006

CP in Bioinformatics

View full text Add to dashboard Cite

RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a web server, as a program with a graphical user interface, or as a set of command line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the web server or the graphical user interface) and prediction of high affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface).

show abstract

“…This may be done by checking the stability of the secondary structure formed (stable means not a good candidate). MFOLD (Zuker et al, 1999), Vienna RNAfold (Hofacker, 2003) and Smith-Waterman (Smith and Waterman, 1981) algorithms have been used in Bozdech et al (2003), Rouillard et al (2003), Matveeva et al (2003), Wright and Church (2002) for this purpose. 4 Other algorithms (Li and Stormo, 2001;Tolonen et al, 2002;Relogio et al, 2002;Sung and Lee, 2003;Rahmann, 2002) directly check sensitivity by eliminating probes that are self-complementary.…”

Section: Previous Workmentioning

confidence: 99%

Randomized probe selection algorithm for microarray design

Gąsieniec

Sant

et al. 2007

Journal of Theoretical Biology

View full text Add to dashboard Cite

DNA microarray technology, originally developed to measure the level of gene expression, has become one of the most widely used tools in genomic study. The crux of microarray design lies in how to select a unique probe that distinguishes a given genomic sequence from other sequences. Due to its significance, probe selection attracts a lot of attention. Various probe selection algorithms have been developed in recent years. Good probe selection algorithms should produce a small number of candidate probes. Efficiency is also crucial because the data involved are usually huge. Most existing algorithms are usually not sufficiently selective and quite a large number of probes are returned. We propose a new direction to tackle the problem and give an efficient algorithm based on randomization to select a small set of probes and demonstrate that such a small set of probes is sufficient to distinguish each sequence from all the other sequences. Based on the algorithm, we have developed probe selection software RANDPS, which runs efficiently in practice. The software is available on our website (http://www.csc.liv.ac.uk/$cindy/RandPS/RandPS.htm). We test our algorithm via experiments on different genomes (Escherichia coli, Saccharamyces cerevisiae, etc.) and our algorithm is able to output unique probes for most of the genes efficiently. The other genes can be identified by a combination of at most two probes.

show abstract

Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide

Cited by 943 publications

References 36 publications

Mutations affecting transcription pausing in the Bacillus subtilis pyr operon

Mutations affecting transcription pausing in the Bacillus subtilis pyr operon

RNA Secondary Structure Analysis Using RNAstructure

Randomized probe selection algorithm for microarray design

Contact Info

Product

Resources

About