Wikiomics:RNA secondary structure prediction - Revision history

Darek Kedra: wikipedia link

2008-05-14T14:43:54Z

wikipedia link

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-		+	==See also==
-	{{Paul P. Gardner}}	+	* [http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software List@wikipedia] by the same author (Paul P. Gardner)

Francois Major: /* Miscellaneous */

2008-05-13T19:30:30Z

Miscellaneous

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	===Miscellaneous===		===Miscellaneous===
-	* [http://www.biophys.uni-duesseldorf.de/stral/about.php StrAl] is an alignment tool designed to provide multiple alignments of non-coding RNAs following a fast progressive strategy. It combines the thermodynamic base pairing information derived from RNAfold calculations in the form of base pairing probability vectors with the information of the primary sequence.	+	* [http://www.biophys.uni-duesseldorf.de/stral/about.php StrAl] is an alignment tool designed to provide multiple alignments of non-coding RNAs following a fast progressive strategy. It combines the thermodynamic base pairing information derived from RNAfold calculations in the form of base pairing probability vectors with the information of the primary sequence.
		+	* [http://www.major.iric.ca/MC-Sym MC-Sym] produces RNA 3-D structures from an input script generated by MC-Fold (above).

Francois Major: /* Single sequence structure prediction */

2008-05-13T19:27:28Z

Single sequence structure prediction

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	One of the issues when predicting RNA secondary structure is that the standard recursions (eg. Nussinov/Zuker-Stiegler) exclude [http://en.wikipedia.org/wiki/Pseudoknot pseudoknots]. Elena Rivas and Sean Eddy published a dynamic programming algorithm that could handle pseudoknots <cite>RIVA99</cite>. However, the time and memory requirements of the method are prohibitive. This has prompted several researches to implement versions of the algorithm that restrict the classes of pseudoknots, resulting in gains in performance.		One of the issues when predicting RNA secondary structure is that the standard recursions (eg. Nussinov/Zuker-Stiegler) exclude [http://en.wikipedia.org/wiki/Pseudoknot pseudoknots]. Elena Rivas and Sean Eddy published a dynamic programming algorithm that could handle pseudoknots <cite>RIVA99</cite>. However, the time and memory requirements of the method are prohibitive. This has prompted several researches to implement versions of the algorithm that restrict the classes of pseudoknots, resulting in gains in performance.
		+
		+	Another issue when predicting RNA secondary structure is the absence of the non-canonical base pairing interactions, such as AA, AC, AG, CC, CU, etc. In order to remedy this problem, Parisien and Major proposed a radically different approach where 19 fundamental nucleotide cyclic motifs are systematically assigned and scored, rather than the classical tandems of base pairs <cite>PARI08</cite>.

	[[Image:yeast.png\|thumb\|S. cerevisiae tRNA-PHE structure space: the energies and structures were calculated using RNAsubopt and the structure distances computed using RNAdistance.]]		[[Image:yeast.png\|thumb\|S. cerevisiae tRNA-PHE structure space: the energies and structures were calculated using RNAsubopt and the structure distances computed using RNAdistance.]]

Francois Major: /* Aligning RNA structures */

2008-05-13T19:03:20Z

Aligning RNA structures

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	* [http://bibiserv.techfak.uni-bielefeld.de/rnaforester/ RNAforester] Compare and align RNA secondary structures via a "forest alignment" approach.		* [http://bibiserv.techfak.uni-bielefeld.de/rnaforester/ RNAforester] Compare and align RNA secondary structures via a "forest alignment" approach.
	* [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/submission.html RNAshapes] the "consensus shapes" method independently enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences.		* [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/submission.html RNAshapes] the "consensus shapes" method independently enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences.
-	* [http://exon.umdnj.edu/software/RSmatch/ RSmatch] provides a light-weight approach to compare RNA structures, thereby uncovering functional structure elements. Compared with other tools for RNA structure comparison, RSmatch is fast, requiring quadratic time determined by the sizes of two given structures.	+	* [http://exon.umdnj.edu/software/RSmatch/ RSmatch] provides a light-weight approach to compare RNA structures, thereby uncovering functional structure elements. Compared with other tools for RNA structure comparison, RSmatch is fast, requiring quadratic time determined by the sizes of two given structures.
		+	* [http://www.major.iric.ca/MC-Cons MC-Cons] assigns to each sequence one of its suboptimal predictions that globally optimizes the sum of pair-wise similarities, resulting in a global and structural consensus assignment (that may include more than one structures).
	====with pseudoknots====		====with pseudoknots====
	* [http://phmmts.dna.bio.keio.ac.jp/pstag/ PSTAG] Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.		* [http://phmmts.dna.bio.keio.ac.jp/pstag/ PSTAG] Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.

Francois Major: /* with pseudoknots */

2008-05-13T19:02:44Z

with pseudoknots

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	====with pseudoknots====		====with pseudoknots====
	* [http://phmmts.dna.bio.keio.ac.jp/pstag/ PSTAG] Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.		* [http://phmmts.dna.bio.keio.ac.jp/pstag/ PSTAG] Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.
-	* [http://www.major.iric.ca/MC-Cons MC-Cons] assigns to each sequence one of its suboptimal predictions that globally optimizes the sum of pair-wise similarities, resulting in a global and structural consensus assignment (that may include more than one structures).

	===Miscellaneous===		===Miscellaneous===

Francois Major: /* Aligning RNA structures */

2008-05-13T19:02:17Z

Aligning RNA structures

←Older revision		Revision as of 19:02, 13 May 2008
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	====with pseudoknots====		====with pseudoknots====
	* [http://phmmts.dna.bio.keio.ac.jp/pstag/ PSTAG] Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.		* [http://phmmts.dna.bio.keio.ac.jp/pstag/ PSTAG] Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.
		+	* [http://www.major.iric.ca/MC-Cons MC-Cons] assigns to each sequence one of its suboptimal predictions that globally optimizes the sum of pair-wise similarities, resulting in a global and structural consensus assignment (that may include more than one structures).

	===Miscellaneous===		===Miscellaneous===

Francois Major: /* References */

2008-05-13T18:55:48Z

References

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	#KNUD03 pmid=12824339		#KNUD03 pmid=12824339
	#HOFA02 pmid=12079347		#HOFA02 pmid=12079347
		+	#PARI08 pmid=18322526
	</biblio>		</biblio>

Francois Major: /* with suboptimal predictions */

2008-05-13T18:54:22Z

with suboptimal predictions

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	* [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/submission.html RNAshapes] Unique suboptimal structures (shapes) are selected based on an abstract representation of RNA secondary structure which is inspired by the dot bracket representation known from the Vienna RNA package. The user can choose from 5 different types of shape resolution corresponding to different abstraction levels.		* [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/submission.html RNAshapes] Unique suboptimal structures (shapes) are selected based on an abstract representation of RNA secondary structure which is inspired by the dot bracket representation known from the Vienna RNA package. The user can choose from 5 different types of shape resolution corresponding to different abstraction levels.
	* [http://clavius.bc.edu/clotelab/RNALOSS/ RNALOSS] locally optimal secondary structure computation. RNALOSS computes the number of k-locally optimal secondary structures for the input RNA, along with relative density of states and minimum free energy of a sample k-locally optimal secondary structure.		* [http://clavius.bc.edu/clotelab/RNALOSS/ RNALOSS] locally optimal secondary structure computation. RNALOSS computes the number of k-locally optimal secondary structures for the input RNA, along with relative density of states and minimum free energy of a sample k-locally optimal secondary structure.
		+	* [http://www.major.iric.ca/MC-Fold MC-Fold] produces all suboptimal secondary structures within a user defined energy percent above the minimum free energy (MFE).

	==Comparative structure prediction==		==Comparative structure prediction==

Francois Major: /* with pseudoknots */

2008-05-13T18:52:15Z

with pseudoknots

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	* [http://bioinformatics.ist.unomaha.edu:8080/x/PLMM_DPSS.html PLMM-DPSS] High sensitivity RNA pseudoknot prediction using "Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking".		* [http://bioinformatics.ist.unomaha.edu:8080/x/PLMM_DPSS.html PLMM-DPSS] High sensitivity RNA pseudoknot prediction using "Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking".
	* [http://www.cs.sfu.ca/~hhtsang/personal/ SARNA-Predict-pk] A heuristic algorithm based on Simulated Annealing for RNA secondary structure prediction including pseudoknots.		* [http://www.cs.sfu.ca/~hhtsang/personal/ SARNA-Predict-pk] A heuristic algorithm based on Simulated Annealing for RNA secondary structure prediction including pseudoknots.
		+	* [http://www.major.iric.ca/MC-Fold MC-Fold] includes an option for H-type pseudo-knots.

	====with suboptimal predictions====		====with suboptimal predictions====

Francois Major: /* External links to RNA folding software */

2008-05-13T18:50:55Z

External links to RNA folding software

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	* [http://www.bioinfo.rpi.edu/applications/sfold/srna.pl Sfold] Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities.		* [http://www.bioinfo.rpi.edu/applications/sfold/srna.pl Sfold] Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities.
	* [http://www.rna.it-chiba.ac.jp/~vsfold/vsfold4/ Vsfold4] folds single RNA sequences using an extended energy model.		* [http://www.rna.it-chiba.ac.jp/~vsfold/vsfold4/ Vsfold4] folds single RNA sequences using an extended energy model.
		+	* [http://www.major.iric.ca/MC-Fold MC-Fold] folds single RNA sequences producing secondary structures that include Watson-Crick and non-canonical base pairs.

	====with pseudoknots====		====with pseudoknots====