University Freiburg

Software/Server

Server and Web-Applications

CPSP web tools
Tools for lattice proteins in the HP-model in various lattice.

• HPstruct	Optimal structure prediction	(» download)
• HPview	Structure visualization	(» download)
• HPdeg	Degeneracy calculation	(» download)
• HPnnet	Neutral network expansion	(» download)
• HPdesign	Sequence design (inverse folding)	(» download)
• LatFit	Lattice models of PDB structures	(» download)

FCC-HP protein

Freiburg RNA tools
RNA related tools from the Freiburg Bioinformatics Group

• CRISPRmap	CRISPR repeat conservation and diversity analysis	New!
• CopraRNA	sRNA target prediction utilizing homology	New! (» download)
• LocARNA	Global and local alignment of RNAs	(» download) (» movie)
• Carna	Alignment of structure ensembles
• ExpaRNA	Exact matching of sequence-structure motives	(» download) (» movie)
• IntaRNA	RNA-RNA interaction prediction	(» download) (» movie)
• INFO-RNA	Inverse folding of RNA / Sequence Design	(» download)
• MARNA	Fixed structure alignment	(» download)

RNA motif

SECISDesign - A Server to Design SECIS-Elements within the Coding Sequence

Software and Libraries

	GraphClust - Large Scale structural clustering of RNA sequences (download).
	LocalFold source code
	CopraRNA source code bundle for local installation: CopraRNA - 1.1.0 (2013-05-07)
	IntaRNA - 1.2.5 (2011-06-10) - Efficient target prediction incorporating accessibility of interaction sites. IntaRNA requires the library of the Vienna RNA Package (versions 1.8.2 - 1.8.5 are supported). The Vienna RNA Package in version 1.8.5 is provided here. If you use IntaRNA, please cite our article. Copyright by Anke Busch and Andreas S. Richter, 2008-2011.
	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.
	ExpaRNA - 1.0 (2013-01-08) 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]; compiles with Gnu C++ Compiler 4.x. Copyright by Steffen Heyne, 2008-2013. 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 1.0: bugfix, >1000 constraints in output file possible!
	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.
	MARNA source code - enables Multiple Alignment of RNAs with fixed/given structures.
	MEMERIS source code
	CPSP-tools - Constraint-based Protein Structure Prediction tools
	ELL - Energy Landscape Library
	BIU - Bioinformatic Utility Library
	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.
	RNA Energy Landscape Tools
	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 .
	CTE-Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination. Copyright by Sebastian Will.