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DotKnot Submission - Input Form

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. DotKnot: pseudoknot prediction including kissing hairpins. Is a heuristic method for pseudoknot prediction. In a given RNA sequence. DotKnot extracts stem regions from the secondary structure probability dot plot.

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DotKnot Submission - Input Form | dotknot.csse.uwa.edu.au Reviews

<META> DESCRIPTION

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. DotKnot: pseudoknot prediction including kissing hairpins. Is a heuristic method for pseudoknot prediction. In a given RNA sequence. DotKnot extracts stem regions from the secondary structure probability dot plot.

<META> KEYWORDS

1 faculty home

2 school home

3 bioinformatics research group

4 knotseeker

5 references

6 manual

7 pseudoknot types

8 local pseudoknots

9 download

10 manual pdf

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faculty home,school home,bioinformatics research group,knotseeker,references,manual,pseudoknot types,local pseudoknots,download,manual pdf,energy parameters,testset,testset1,testset2,dotknot,calculated by rnafold,for h type pseudoknot,if kissing hairpins

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DotKnot Submission - Input Form | dotknot.csse.uwa.edu.au Reviews

https://dotknot.csse.uwa.edu.au

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. DotKnot: pseudoknot prediction including kissing hairpins. Is a heuristic method for pseudoknot prediction. In a given RNA sequence. DotKnot extracts stem regions from the secondary structure probability dot plot.

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dotknot.csse.uwa.edu.au

1

DotKnot - Manual

http://dotknot.csse.uwa.edu.au/manual.html

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. We set the maximum sequence length limit for online submission to 1000 bases. For H-type pseudoknots and to 400 bases. Please provide a sequence ID for future reference. Paste your sequence in plain format.

2

DotKnot - Pseudoknot Types

http://dotknot.csse.uwa.edu.au/pseudoknot_types.html

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. DotKnot includes the class of recursive H-type pseudoknots. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. The user can choose whether kissing hairpins.

3

DotKnot - Manual

http://dotknot.csse.uwa.edu.au/near-optimal-pseudoknots.html

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. In addition to the best global. Folding, the best local. DotKnot returns the best pseudoknots in terms of estimated free energy to length ratio. The desired pseudoknot structure is found:. Position: 1 . 33.

4

DotKnot - Archive

http://dotknot.csse.uwa.edu.au/archive.html

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. DotKnot 1.1.tar.gz. Show the best near-optimal pseudoknots. DotKnot 1.2.tar.gz. Prediction of kissing hairpins. Show the predicted global structure. DotKnot 1.2.1.tar.gz. DotKnot 1.3.tar.gz.

5

DotKnot - Pseudoknot Types

http://dotknot.csse.uwa.edu.au/references.html

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. If you find DotKnot useful for your research, please cite:. J Sperschneider and A. Datta. DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. 2010; 38(7): e103.

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bioinfo.csse.uwa.edu.au

Bioinformatics at UWA

http://bioinfo.csse.uwa.edu.au/software.html

Study Bioinformatics at UWA. Software and Web Servers. For the prediction of certain types of RNA pseudoknots using the secondary structure probability dot plot. A web server is available for pseudoknot prediction over the internet. The maximum sequence length limit is set to 1000 bases for online submission. The algorithm has been implemented in Python ( http:/ www.python.org. Http:/ dotknot.csse.uwa.edu.au. 2010; 38(7):e103. Abstract. Http:/ knotseeker.csse.uwa.edu.au. Is a program for aligning multipl...

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DotKnot Submission - Input Form

Input and Output Format. Code [DotKnot 1.3.2.tar.gz]. DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006. Sequences and structures used for evaluation in the papers. For comments, suggestions and reporting bugs please contact janaspe(at)csse.uwa.edu.au. DotKnot: pseudoknot prediction including kissing hairpins. Is a heuristic method for pseudoknot prediction. In a given RNA sequence. DotKnot extracts stem regions from the secondary structure probability dot plot.

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