Software and Web Servers

DotKnot

dotknot

We developed DotKnot 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).

Web Server: http://dotknot.csse.uwa.edu.au
References:
J. Sperschneider, A. Datta and M.J. Wise. Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins. RNA. 2011. Advance Access
J. Sperschneider and A. Datta. DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. Nucleic Acids Research. 2010; 38(7):e103. Abstract

KnotSeeker

pseudoknot

We developed KnotSeeker for the detection of pseudoknots in RNA sequences. The algorithm has been implemented in Python (http://www.python.org). A web server is available for pseudoknot detection over the internet. The maximum sequence length limit is set to 1000 bases for online submission. If you want to run KnotSeeker on your local machine for longer sequences, feel free to download and install the code.

Web Server: http://knotseeker.csse.uwa.edu.au
Download: http://knotseeker.csse.uwa.edu.au/download.html
Reference: J. Sperschneider and A. Datta. KnotSeeker: Heuristic pseudoknot detection in long RNA sequences. RNA. 2008; 14(4): 630-40. Abstract

MASON

mason

MASON is a program for aligning multiple DNA or protein sequence alignment. MASON is a parallelized version of ClustalW and runs in parallel on a workstation cluster. The MASON source code can also be downloaded.

Download: mason.tar
Reference: J. Ebedes and A. Datta. Multiple sequence alignment in parallel on a workstation cluster. Bioinformatics. 2004; 20(7): 1193-5. Abstract