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INFO-RNA - A Server for Inverse Folding of RNA | |
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SECISDesign - A Server to Design SECIS-Elements within the Coding Sequence | |
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CPSP web tools
(Note: BETA version ... please report bugs!)
Includes: Optimal protein structure prediction in the HP-model, Viewing, Conversion between structure representations, ... |
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MARNA - A Server for Multiple Alignment of RNAs |
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TassDB - TAndem Splice Site DataBase | |
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NIPU server - Display splicing regulatory motifs and single-stranded mRNA regions | |
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BioBayesNet - a web server for feature extraction and bayesian network modeling of biological sequence data | |
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LocARNA Server (@ TBI) - Multiple Alignment of RNAs |
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IntaRNA - 1.2.2 (2009-09-30)
NEW Version - Efficient Target Prediction Incorporating Accessibility of Target Sites
Default parameters have changed with version 1.2.
To use IntaRNA, you need the library of the Vienna RNA Package (version ≥1.8.2). The latest version of the Vienna RNA Package version can be downloaded here. If you use our tool for your own scientific publication, please cite our article. Copyright by Anke Busch and Andreas S. Richter, 2008-2009. |
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LocARNA - Local Alignment of RNA.
A tool for pairwise and multiple, global and local alignment of RNA
with simultaneous folding.
Copyright by Sebastian Will, 2006-2009. |
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ExpaRNA - 0.8 (2009-03-18) - formerly RNAexact)
C++ implementation to find the longest common subsequence of exact pattern matchings (LCS-EPM problem)
of two RNAs given with their primary and secondary structure (mfe-structure is used if no structure is available).
Source is available as [tar.gz] or [zip]; compiles with Gnu C++ Compiler 4.x. Copyright by Steffen Heyne, 2008-2009. If you use ExpaRNA, please cite our article. To use ExpaRNA, you need the library of the Vienna RNA Package that can be downloaded here. ExpaRNA compiles also under cygwin for Windows! usage example: ExpaRNA -L Examples/HCVirus_IRES_RNAs.fa New in 0.8: Another nasty EPM bug is fixed, no open bugs anymore New in 0.7.7: gaps are ignored in input sequences New in 0.7.6: EPM bug-fix!!! start with new EPM scoring, see "-t" option New in 0.7.1: EPM output (-e option), bug-fixes New in 0.6: FASTA file input, LocARNA constrained output, removed XERCES-C dependency, code clean-up |
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INFO-RNA
- A Fast Approch to Inverse RNA Folding Satisfying Sequence Constraints
INFO-RNA-2.1.tar.gz
is available. Its a slightly modified version, which allows to design a random initializing sequence.
Older source is available as : INFO-RNA-2.0.tar.gz ( version 1.0 ). To use INFO-RNA, you need the library of the Vienna RNA Package that can be downloaded here. Copyright by Anke Busch, 2006-2007. |
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MEMERIS source code | |
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CPSP-tools - Constraint-based Protein Structure Prediction tools |
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ELL - Energy Landscape Library |
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BIU - Bioinformatic Utility Library |
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LatPack Tools and LatFit
C++ implementation of folding simulations approaches for arbitrary
lattice protein models as well as fitting of 3D PDB structures onto
lattices.
Copyright by Martin Mann, 2008. |
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RNA Energy Landscape Tools |
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Local Sequence Structure Aligment.
C++ implementation for our paper
Local Sequence-Structure Motifs in RNA
Please cite this article, if you use the program for a publication. Source is available as [tar.gz] or [zip]; compiles with Gnu C++ Compiler 3.x. Copyright Sebastian Will . |
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CTE-Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination.
Copyright by Sebastian Will. |
