Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
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* Corresponding author: David H Mathews david_mathews@urmc.rochester.edu
BMC Bioinformatics 2006, 7:173 doi:10.1186/1471-2105-7-173
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Research
Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I Shaw, Ying-Wai Li, Russell L Malmberg, Liming Cai BMC Bioinformatics 2012, 13(Suppl 5):S1 (12 April 2012) |
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Software
RNAstructure: software for RNA secondary structure prediction and analysis Jessica S Reuter, David H Mathews BMC Bioinformatics 2010, 11:129 (15 March 2010) |
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Research article
Akito Taneda BMC Bioinformatics 2008, 9:521 (5 December 2008) |
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Methodology article
Dinucleotide controlled null models for comparative RNA gene prediction Tanja Gesell, Stefan Washietl BMC Bioinformatics 2008, 9:248 (27 May 2008) |
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Methodology article
A novel representation of RNA secondary structure based on element-contact graphs Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang BMC Bioinformatics 2008, 9:188 (11 April 2008) |
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Research article
Strategies for measuring evolutionary conservation of RNA secondary structures Andreas R Gruber, Stephan H Bernhart, Ivo L Hofacker, Stefan Washietl BMC Bioinformatics 2008, 9:122 (26 February 2008) Simple metrics of folding energy and optimal structures accurately measure evolutionary conservation of RNA secondary structure and should form the basis of tools to predict non-coding RNAs, whereas complex methods fail to improve performance.
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Research article
Vincent M Ulvé, Emeric W Sevin, Angélique Chéron, Frédérique Barloy-Hubler BMC Genomics 2007, 8:467 (19 December 2007) |
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Methodology article
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign Arif Harmanci, Gaurav Sharma, David H Mathews BMC Bioinformatics 2007, 8:130 (19 April 2007) |
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Research article
Considerations in the identification of functional RNA structural elements in genomic alignments Tomas Babak, Benjamin J Blencowe, Timothy R Hughes BMC Bioinformatics 2007, 8:33 (30 January 2007) Search tools perform poorly at finding noncoding RNAs on a test set of known ncRNAs for which the sequences are randomly shuffled, although a combination of conservation and thermodynamic stability has promise for ncRNA detection.
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Methodology article
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints Robin D Dowell, Sean R Eddy BMC Bioinformatics 2006, 7:400 (4 September 2006) When predicting RNA secondary structure, constraining the Sankoff folding and alignment algorithm by using confidently aligned positions, or pins, speeds up the algorithm and lowers memory requirements without harming performance.
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