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EffectiveDB

Dept of Microbiology and Ecosystem Science. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. A new version 5.1 of EffectiveELD has been finished. It is based on Pfam 29.0 (within Interpro 5.18-57.0). The genome repository was created from the bacterial NCBI RefSeq as of June 2016 and by using the genome metadata from the . Search and export tool. New release 5.0 of Eukaryotic-like domains finished. Protein domains have been annotated using Interproscan 53.0. Search and export tool.

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Dept of Microbiology and Ecosystem Science. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. A new version 5.1 of EffectiveELD has been finished. It is based on Pfam 29.0 (within Interpro 5.18-57.0). The genome repository was created from the bacterial NCBI RefSeq as of June 2016 and by using the genome metadata from the . Search and export tool. New release 5.0 of Eukaryotic-like domains finished. Protein domains have been annotated using Interproscan 53.0. Search and export tool.

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EffectiveDB | effectivedb.org Reviews

https://effectivedb.org

Dept of Microbiology and Ecosystem Science. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. A new version 5.1 of EffectiveELD has been finished. It is based on Pfam 29.0 (within Interpro 5.18-57.0). The genome repository was created from the bacterial NCBI RefSeq as of June 2016 and by using the genome metadata from the . Search and export tool. New release 5.0 of Eukaryotic-like domains finished. Protein domains have been annotated using Interproscan 53.0. Search and export tool.

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EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29 | EffectiveDB

http://www.effectivedb.org/news/effectiveeld-5-1-eukaryotic-like-domain-prediction-upgraded-to-pfam-29

Dept of Microbiology and Ecosystem Science. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. A new version 5.1 of EffectiveELD has been finished. It is based on Pfam 29.0 (within Interpro 5.18-57.0). The genome repository was created from the bacterial NCBI RefSeq as of June 2016 and by using the genome metadata from the GOLD database as of June 2016. Search and export tool. Prediction of microbial phenotypes based on comparative genomics. 43 1 4277 76681. 43 1 4277 876681.

3

News | EffectiveDB

http://www.effectivedb.org/news

Dept of Microbiology and Ecosystem Science. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. A new version 5.1 of EffectiveELD has been finished. It is based on Pfam 29.0 (within Interpro 5.18-57.0). The genome repository was created from the bacterial NCBI RefSeq as of June 2016 and by using the genome metadata from the . Search and export tool. New release 5.0 of Eukaryotic-like domains finished. Protein domains have been annotated using Interproscan 53.0. Search and export tool.

4

| EffectiveDB

http://www.effectivedb.org/effective/browse

Dept of Microbiology and Ecosystem Science. EffectiveDB provides precalculated results for all 1676 bacterial genomes in the EggNOG 4.0. Database and additional 23 bacterial genomes from the NCBI RefSeq datase. In the near future we will switch to the upcoming EggNOG 5.0 database, derived from STRING 11 (about 10.000 genomes). RefSeq genomes not contained in STRING will be continuously added. We have used the following settings:. EffectiveELD: enabled, minimal Z-score=4. Nevskia soli DSM 19509. Caldalkal...

5

EffectiveT3 | EffectiveDB

http://www.effectivedb.org/method/effectivet3

Dept of Microbiology and Ecosystem Science. Prediction of secreted proteins. The new model is now embedded into Effective and also available for download. The default minimal score from the Naive Bayesian Classifier for the class ‘secreted’ is 0.9999 in the new model. This default value is called ‘selective’ at the webpage, whereas 0.95 is called ‘sensitive’. The threshold can also be freely chosen. Evaluation of the new EffectiveT3 model 2.0 and comparison to the previous model 1.0. EffectiveDB-updates ...

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cube.univie.ac.at

Master studies | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/master-studies

Bachelor and master projects. CUBE contributes to multiple master programs in biology and computational science. We are engaged in designing the upcoming Master Bioinformatics at our university. We recommend the master programs "Computational Science" and "Microbial Ecology" particularly for students who are interested in doing their master thesis at CUBE. The master program in bioinformatics is open to students having a bachelor degree in life science, mathematics or computer science. Master program Mol...

cube.univie.ac.at

Publications | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/publications

Bachelor and master projects. The fulltext of publications might not be freely accessible but require subscription. Please request reprints at contact.cube@univie.ac.at. Publications in peer reviewed journals. NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. Grebien F, Rattei T. The R package is freely available under https:/ github.com/Edert/NVT. CONTACT: thomas.rattei@univie.ac.atSupplementary. Information: Supplementary data are available at Bioinformatics online.

cube.univie.ac.at

Open positions | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/open-positions

Bachelor and master projects. The Division of Computational Systems Biology at the University of Vienna is offering a. Group Leader Position in Bioinformatics. The Group leader will actively contribute to teaching in bioinformatics, perform independent research in bioinformatics and contribute to the self-administration of the university. Depending on the performance in research and education, the possibility of a postdoctoral lecture qualification ( venia legendi ) will be provided. Read more. We encour...

cube.univie.ac.at

Lecture series | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/lecture-series

Bachelor and master projects. Searching for Influencers via Optimal Percolation: from Twitter to the Brain. City College of New York. Exploring viral diversity through (meta-) genomics: towards a thorough characterization of the unseen majority. Sullivan Lab, Department of Microbiology. Analysis of the genome of sugar beet: Current status, next steps. Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU). Chloroplast I/O: RNA editing, effectors and evolution. Deep metageno...

cube.univie.ac.at

Prof. Dr. Thomas Rattei | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/people/thomas-rattei

Bachelor and master projects. Prof Dr. Thomas Rattei. Head of the Division of Computational Systems Biology. Vice-head of the Department of Microbiology and Ecosystem Science. 43 1 4277 76680. Thomas.rattei@univie.ac.at. Dr Ing. Alexander Platzer. NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. Publications: Prof. Dr. Thomas Rattei.

cube.univie.ac.at

News | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/news

Bachelor and master projects. Job opening: Group Leader Position. The Division of Computational Systems Biology at the University of Vienna is offering a. Group Leader Position in Bioinformatics. CUBE - the division of Computational Systems Biology. Is part of the Department of Microbiology and Ecosystem Science of the . Virus Orthologous Groups: A novel resource for virus (meta)genomics. Normalization visualization tool (NVT) released. Public release of CONSPRED genome annotation pipeline. CONSPRED is a...

cube.univie.ac.at

Bachelor and master thesis projects | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/bachelor-and-master-thesis-projects

Bachelor and master projects. Bachelor and master thesis projects. The practical course "300224 PP Genome analysis of prokaryots - applied bioinformatics for the analysis of a genome sequence" is well suited for a bachelor project in the Biology curriculum. For bachelor theses in other curricula please contact Thomas Rattei. Thesis project example 1: Extraction of prokaryotic phenotypes from literature. THESIS PROJECT EXAMPLE 2: SUPERVISED machine Learning for PHENOTYPE prediction. We have developed geno...

cube.univie.ac.at

Staff | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/people

Bachelor and master projects. Category (field tr staff category). Prof Dr. Thomas Rattei. Head of the Division of Computational Systems Biology. Vice-head of the Department of Microbiology and Ecosystem Science. 43 1 4277 76680. Thomas.rattei@univie.ac.at. 43 1 4277 76682. Florian.goldenberg@univie.ac.at. 43 1 4277 76681. Gabriele.kaindl@univie.ac.at. Thomas.nussbaumer@univie.ac.at. Dr Ing. Alexander Platzer. Alexander.platzer@univie.ac.at. Contact.cube@univie.ac.at. Contact.cube@univie.ac.at. Deep metag...

cube.univie.ac.at

Similarity Matrix of Proteins (SIMAP) | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/resources/simap

Bachelor and master projects. Similarity Matrix of Proteins (SIMAP). SIMAP - The similarity matrix of proteins. The similarity matrix of proteins is a database of protein sequences, their all-against-all sequence similarities and functional annotations. The database is currently re-implemented, based on a different algorithm for sequence similarity calculation. SIMAP 1 refers to the traditional database, run from 2004 until 2014. SIMAP 2 is the new SIMAP database which has started in 2015. The new SIMAP ...

cube.univie.ac.at

CUBE & friends BBQ on July 2 | CUBE - Bioinformatics and Computational Systems Biology, University of Vienna

http://cube.univie.ac.at/news/cube-friends-bbq-on-july-2

Bachelor and master projects. CUBE and friends BBQ on July 2. We celebrate 5 years of CUBE and invite all recent and former CUBE members and our friends to a BBQ party on Thursday July 2nd. The party will start around 5pm on our terrace. NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.

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EffectiveDB

Dept of Microbiology and Ecosystem Science. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. A new version 5.1 of EffectiveELD has been finished. It is based on Pfam 29.0 (within Interpro 5.18-57.0). The genome repository was created from the bacterial NCBI RefSeq as of June 2016 and by using the genome metadata from the . Search and export tool. New release 5.0 of Eukaryotic-like domains finished. Protein domains have been annotated using Interproscan 53.0. Search and export tool.

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