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BioBayesNet - a web server for feature extraction and bayesian network modeling of biological sequence data | |||||||||||||||||||
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CPSP web tools
(New version !)
Tools for lattice proteins in the HP-model in various lattice.
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Freiburg RNA tools
(New !!!)
RNA related tools from the Freiburg Bioinformatics Group
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INFO-RNA - A Server for Inverse Folding of RNA | |||||||||||||||||||
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MARNA - A Server for Multiple Alignment of RNAs |
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SECISDesign - A Server to Design SECIS-Elements within the Coding Sequence | |||||||||||||||||||
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NIPU server - Display splicing regulatory motifs and single-stranded mRNA regions | |||||||||||||||||||
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TassDB - TAndem Splice Site DataBase |
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LocalFold source code | |
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IntaRNA - 1.2.5 (2011-06-10)
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, 2008-2011. |
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LocARNA - Global and 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 - 0.8.3 (2011-02-25)
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, 2008-2011. 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 Examples/HCVirus_IRES_RNAs.fa New in 0.8.3: Command line options changed! 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-2.1.2.tar.gz
is available (12-April-2011) [minor bugfix for hairpin loops of size >30bp]
Older source is available as version : 2.1.1, 2.1.0, 2.0, 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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MARNA source code - enables Multiple Alignment of RNAs with fixed/given structures. | |
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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. |