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...
dotknot.csse.uwa.edu.au
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.
dotknot.csse.uwa.edu.au
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.
rnaparse.com
Pseudoknots
http://www.rnaparse.com/Pseudoknots.html
The methods we use here essentially ignore rna molecular energy and “look” or match a specific configuration which can then be further verified via slower and more computationally expensive methods. This grammatical method bypasses the NP problem of trying every possible fitting permutation by instead matching a predefined system of stems and loops in a linear fashion. Http:/ rnavlab.utep.edu/portal rna searchable database. Http:/ www.ekevanbatenburg.nl/PKBASE/PKB.HTML Pseudobase. A context-sensitive gra...
dotknot.csse.uwa.edu.au
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.
dotknot.csse.uwa.edu.au
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.
dotknot.csse.uwa.edu.au
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.
