Name: FreiburgRnaTools
Owner: Bioinformatics Lab - Department of Computer Science - University Freiburg
Description: Issue tracking etc. for Freiburg RNA tools webserver
Created: 2017-02-13 09:59:21.0
Updated: 2017-02-13 09:59:21.0
Pushed: 2017-11-10 15:30:06.0
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README
The Freiburg RNA Tools webserver is the central ad hoc service of Prof. Rolf Backofen's bioinformatics group to use RNA-related algorithms developed by his or collaborating groups.
This repository is mainly used to collect issues and feature requests for the webserver.
The webserver currently features:
- RNA-RNA interaction prediction:
- CopraRNA for sRNA targeting
- IntaRNA for fast RNA-RNA interaction prediction
- GLASSgo for finding sRNA homologs
- metaMIR to study human miRNA interactions
- Sequence-structure alignment:
- LocARNA for global and local RNA alignment
- CARNA structure ensemble alignment
- MARA alignment based on single fixed structures
- ExpaRNA for identifying sets of local exact matches
- CRISPR-related tools:
- CRISPRmap to study CRISPR conservation
- Sequence design:
- AntaRNA for multi-objective designs, to e.g. restrict GC-content
- INFORNA stability-focused design
- SECISDesign inserts SECIS-elements into mRNAs
- Splicing:
- NIPU to find splicing regulatory motifs
Furthermore, we provide a teaching related section with JS implementations of various bioinformatics algorithms:
- Nested RNA structure prediction
- nested structure counting
- maximal base pair structure prediction via the Nussinov algorithm with different recursions
- base pair probability and unpaired probability computation via a variant of the McCaskill algorithm
- maximum expected accuracy (MEA) structure prediction
- RNA-RNA interaction prediction
- co-folding approach via Nussinov-variant
- maximal hybrid-only intermolecular base pair interaction prediction
- accessibility-incorporating interaction prediction
- General sequence alignment approaches
- Needleman-Wunsch (global, linear gap costs)
- Gotoh (global, affine gap costs)
- Waterman-Smith-Beyer (global, arbitrary gap costs)
- Smith-Waterman (local, linear gap costs)
