Explore @BackofenLab Open Source projects

Bioinformatics Lab - Department of Computer Science - University Freiburg (@BackofenLab)

BackofenLab

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IntaRNA

Efficient target prediction incorporating accessibility of interaction sites

RNA-Playground

Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.

GGL

Graph Grammar Library

CRISPRidentify

CRISPRcasIdentifier

Machine learning for accurate identification and classification of CRISPR-Cas systems

GraphClust-2

A pipeline for structural clustering of RNA secondary structures

CRISPRloci

GraphProt2

Modelling RBP binding preferences to predict RPB binding sites

RNAProt

Modelling RBP binding preferences to predict RPB binding sites

AlgoDat

Algorithm & Data structures

ShaKer

SHApe simulation with graph KERnels

Jupyter Notebook

CRISPRtracrRNA

mechRNA

CAM

Constraint-based Atom-Atom Mapping

SalamiSnake

Snakemake Piepline for CLIP data

DeepAcr

StoatyDive

AxoWise

An integrated graph system of biological entities, functional terms, and publications.

Peakhood

Individual site context extraction for CLIP-Seq peak regions

MICA

Multiple Interval-based Curve Alignment

CRISPRleader

CRISPRleader takes a complete genome or draft genome as input and selects all possible CRISPR arrays in the correct orientation, and annotates the CRISPR leader boundaries.

IntaRNA-benchmark

Data and scripts to benchmark IntaRNA

Casboundary

Automated definition of integral CRISPR/Cas cassettes.

GraphClust

Structural clustering of local RNA secondary structures

local_alignment

Jupyter Notebook

GeneralizedCoarseGraining

Generalized Coarse Graining (GCG) enables the recursive coarse graining of discrete energy landscapes

IntaRNA-benchmark-SHAPE

This repository contains data and analysis scripts for IntARNA's structure probing (SHAPE) extension

Jupyter Notebook

RBPBench

AlgorithmAndDatastructures-Material

Slides for Algorithms and Datastructure lecture for IEMS/ESE

LatPack

Collection of tools related to modelling and folding simulations of lattice-protein models with arbitrary energy functions

docker-galaxy-clip

Docker image with fully functional Galaxy server with tools for CLIP analyses

Accessory.Crispr

Comprehensive search for accessory proteins encoded with archaeal and bacterial Type III CRISPR-Cas gene cassettes reveals 39 new cas gene families

Course_Algorithms_in_Bioinformatics

Interfaces and materials for the programming course "Algorithms in Bioinformatics"

Jupyter Notebook