Lehr- und Forschungseinheit Bioinformatik
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Software

ISAR - Isoform Structure Alignment Representation

Project Website
rab We present an efficient alignment algorithm to construct Isoform Structure Alignment Representations (ISARs) from sets of isoforms, paralogs and orthologs by exploiting information on the gene structure and the phylogeny

Apriori on Patterns

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Tool to search for frequent regular expressions in a database of protein sequences (written in PERL)

CheckShift - A Tool for Rereferencing Chemical Shifts

Project Website
CheckShift is a tool for preprocessing chemical shift data to detect and correct referencing errors.

ConceptMaker - Analyse von Geneexpressionsdaten mit Literaturwissen

Website
ConceptMaker ConceptMaker analysiert Hochdurchsatzdaten um Anfragen gegen einen indizierten Datenbestand zu erzeugen. Damit wird Literaturwissen automatisch in einen funktionellen Zusammenhang mit den Messdaten gebracht. ConceptMaker harnesses large scale measurements such as microarray experiments to automatically construct queries. The queries are then posed against the biomedical literature to retrieve functional relationships relevant for the experiment.

FERN - A Java Framework for Stochastic Simulation and Evaluation of Reaction Networks

Project Website
FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java. It includes state of the art algorithms for stochastic simulation and a powerful visualization system based on gnuplot and Cytoscape.

GGEA - Gene Graph Enrichment Analysis

Project Website

GGEA is an intuitive method to detect consistently and coherently enriched gene sets in gene expression data.

GGEA comes embedded in the EnrichmentBrowser, a multi-functional platform for enrichment analysis that includes a variety of enrichment methods and accompanying visualization capabilites.

HALO - Precise transcript half-life determination in Java

Project Website
HALO is a software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied as well as a graphical user interface, command line tools and a well-documented Java API.

Hybroscale - Computation of hybridization networks

Project Website
Hybroscale Hybroscale is developed specifically for the research of hybridization networks including its computation and visualization. More specifically, the program aims at calculating all phylogenetic networks displaying a set of non-binary input trees with minimum hybridization number.

ISAR - Isoform Structure Alignment Representation

Project Website
We present an efficient alignment algorithm to construct Isoform Structure Alignment Representations (ISARs) from sets of isoforms, paralogs and orthologs by exploiting information on the gene structure and the phylogeny

Manananggal - A Novel Viewer And Detection Method For Alternative Splicing Events

The Manananggal service including dokumentation and a tutorial can be found here.
Manananggal is an application specifically designed for the identification of splicing events in next generation sequencing data. Manananggal includes a web application for visual inspection and a command line tool that allows for ASE detection. Manananggal is a highly interactive web application that offers functions specifically tailored to the identification of alternative splicing events that other tools are lacking. The ability to select a subset of isoforms allows an easier interpretation of complex alternative splicing events. In contrast to SpliceSeq and the DEXSeq splicing plot, Manananggal does not obscure the gene structure by showing full transcript models that makes it easier to determine which isoforms are expressed and which are not.

Manananggal has been developed by Matthias Barann in a cooperation of the LMU with Roche as a postdoc in the RTF program. Fabian Birzele supervised the project at Roche.

MIRTFnet- Analysis of miRNA regulated TFs

Project Website
We develop the method MIRTFnet to determine the experimental conditions where certain regulators like miRNAs become active and how they regulate the transcriptome via cascades of other miRNAs, transcription factors (TFs) or kinases. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions.

ProCope - Protein Complex Prediction and Evaluation

Project Website
ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments.

Quasar

Project Website
A flexible system for scoring and ranking sequence-structure alignments (written in Java).

REA - RIP-chip enrichment analysis

Project Website

This is a collection of methods for (R)IP-chip (E)nrichment (A)nalysis. A table of normalized expression values from a RIP-chip experiment is read (e.g. as produced by the Affymetrix PowerTools) and two main steps are performed: Subtraction of the background of non target genes and secondary normalization for differing IP efficiencies.

RelEx - Extraktion von Objekt-Objekt Wechselwirkungen aus biomedizinischen Texten

Website
RelEx RelEx verwendet den Stanford Dependency Parser, um Abhängigkeitsbäume für Sätze zu berechnen. Durch einige wenige Baumtransformationsregeln werden Relationen und zwischen den ?named entities? extrahiert und zu verschiedenen Relationstypen zugeordnet. RelEx uses semantic dependency trees to extract relations and relation types between named entities from the entire PubMed. Due to the dependency trees only few tree rules are required to harvest a wide range of complex relationship phrases.

SimShiftDB - A Tool for Analyzing Chemical Shifts

Project Website
SimShiftDB is tool that searches for similarities between a target protein with assigned chemical shifts and a database of template proteins for which both chemical shift data and 3D coordinates are available in order to support NMR-spectrocopists.

Syngrep - Suche nach benannten Objekten in biomedizinischen Texten

Website
syngrep syngrep findet benannte biologische Objekte in Freitext. In weniger als 10 Minuten kann die gesamte PubMed Datenbank gleichzeitig auf Hits gegen mehrere Synonymlisten durchsucht werden. syngrep is a fast named entity recognition tool that scans the entire PubMed for matches against multiple synonym lists in less than ten minutes.

Vorolign

Project Website
Fast and flexible structural alignment using Voronoi contacts (Server Version).
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