bioinfo.csse.uwa.edu.au
Bioinformatics at UWA
http://bioinfo.csse.uwa.edu.au/index.html
Study Bioinformatics at UWA. Biology easily has 500 years of exciting problems to work on." - Donald E. Knuth. School of Computer Science and Software Engineering. Bioinformatics is broadly defined as the application of computers for solving information problems in the life sciences. Bioinformatics is commonly associated with the creation and maintenance of databases for the vast amount of information coming from laboratories, for example nucleic acid and protein sequence data. However, bioinformatic...
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...
knotseeker.csse.uwa.edu.au
KnotSeeker - Download
http://knotseeker.csse.uwa.edu.au/download.html
Practical RNA folding including simple recursive pseudoknots. Exact matching under RNA base pairing rules. Toolbox for prediction and comparison of RNA secondary structures. Jana Sperschneider and Amitava Datta. KnotSeeker: Heuristic pseudoknot detection in long RNA sequences. RNA. 2008; 14(4): 630-40. For comments and suggestions contact janaspe(at)csse.uwa.edu.au. KnotSeeker has been implemented in Python. As the next step, download KnotSeeker.py. Version 1.3), GUUGle. If problems occur, see here.
bioinfo.csse.uwa.edu.au
Bioinformatics at UWA
http://bioinfo.csse.uwa.edu.au/news.html
Study Bioinformatics at UWA. Annual Meeting of the RNA Society. June 14-19, 2011. Kyoto, Japan. Http:/ www.rnasociety.org/#RNASocEvents.
bioinfo.csse.uwa.edu.au
Bioinformatics at UWA
http://bioinfo.csse.uwa.edu.au/people.html
Study Bioinformatics at UWA. Academic staff and research students. Academic Staff and Research Students. School of Computer Science and Software Engineering. Http:/ www.csse.uwa.edu.au/ alison/epimap/. Email: alisona(at)csse.uwa.edu.au. Application of bioinformatics to epidemiology - specifically in relation to man-made chemical affects on embryonic development. Toxicogenomics - specifically in using microarray data to investigate effects of low dosage and mixtures of chemical exposures. Low complexity/n...
bioinfo.csse.uwa.edu.au
Bioinformatics at UWA
http://bioinfo.csse.uwa.edu.au/projects.html
Study Bioinformatics at UWA. A Novel Method for Building Phylogenetic Trees. Computing the Genetic Basis for the Sit-and-Wait Hypothesis of Bacterial Pathogenicity. Honours and Masters projects offered in 2010. A Novel Method for Building Phylogenetic Trees. Contact: Prof. Michael Wise. Computing the Genetic Basis for the Sit-and-Wait Hypothesis of Bacterial Pathogenicity. 1 Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology,. 1131-36, John Wiley.
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.
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.