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GenSkew - visualization of nucleotide skew in genome sequences

GenSkew: Genomic nucleotide skew application. GenSkew is an application for computing and plotting nucleotide skew data. It was developed at the TU Munich, Genome oriented bioinformatics. During a 2 weeks-practical in bioinformatics programming by the students Miroslava Edelstein, Florian Gehrke, Sonja Hopf, Andre Jehl and Annahita Oswald, supervised by Thomas Rattei. Since 2010, GenSkew is maintained by the Department of Computational Systems Biology of the University of Vienna. DNA sequence file in FAS...

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GenSkew - visualization of nucleotide skew in genome sequences | genskew.csb.univie.ac.at Reviews

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GenSkew: Genomic nucleotide skew application. GenSkew is an application for computing and plotting nucleotide skew data. It was developed at the TU Munich, Genome oriented bioinformatics. During a 2 weeks-practical in bioinformatics programming by the students Miroslava Edelstein, Florian Gehrke, Sonja Hopf, Andre Jehl and Annahita Oswald, supervised by Thomas Rattei. Since 2010, GenSkew is maintained by the Department of Computational Systems Biology of the University of Vienna. DNA sequence file in FAS...

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1 overview

2 introduction

3 availibility

4 nucleotide1

5 nucleotide2

6 windowsize

7 stepsize

8 resolution

9 system requirements

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GenSkew - visualization of nucleotide skew in genome sequences | genskew.csb.univie.ac.at Reviews

https://genskew.csb.univie.ac.at

GenSkew: Genomic nucleotide skew application. GenSkew is an application for computing and plotting nucleotide skew data. It was developed at the TU Munich, Genome oriented bioinformatics. During a 2 weeks-practical in bioinformatics programming by the students Miroslava Edelstein, Florian Gehrke, Sonja Hopf, Andre Jehl and Annahita Oswald, supervised by Thomas Rattei. Since 2010, GenSkew is maintained by the Department of Computational Systems Biology of the University of Vienna. DNA sequence file in FAS...

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effectivedb.org

Documentation and support | EffectiveDB

http://www.effectivedb.org/help

Dept of Microbiology and Ecosystem Science. Job submission to EffectiveDB. Interpretation of EffectiveDB predictions. Frequently asked questions (FAQ). Q: Why the results with different arguments varies considerably, especially when I add EffectiveS346 arguments? Q: Can I run all these tools you used for the database also locally on new sequences/genomes? A: Yes, our computer cluster would be pleased! Q: What does this 'N.D.' mean, which I see sometimes at 'Gram negative:' and following lines? Prediction...

effectivedb.org

Download | EffectiveDB

http://www.effectivedb.org/download

Dept of Microbiology and Ecosystem Science. Precalculations for bacterial genomes. Browsable folder of results for all bacterial genomes from EggNOG 4.0 and selected additional genomes from NCBI RefSeq by NCBI taxonomy ID. ZIP archive of results for all bacterial EggNOG 4.0 genomes by NCBI taxonomy ID. Tab separated values file listing taxonomyids, names and predicted seretion systems for all bacterial EggNOG 4.0 genomes. Current and previous EffectiveELD. Browsable folder of EffectiveELD releases.

effectivedb.org

Effective job submission | EffectiveDB

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

Dept of Microbiology and Ecosystem Science. Prediction of secreted proteins and protein secretion systems. Main input for your job. Will only be used for job notification and is not stored on the server. One or multiple protein sequences in FASTA format:. FASTA formatted protein sequences. Upload a FASTA formatted protein sequence file. Predicts Type III secreted proteins based on their signal peptide. Select the version of the EffectiveT3. Predicts secreted proteins based on eukaryotic-like domains.

effectivedb.org

New EffectiveDB website | EffectiveDB

http://www.effectivedb.org/news/new-effectivedb-website

Dept of Microbiology and Ecosystem Science. EffectiveDB is now hosted in a new website. It is based on the Drupal. Framework and gives user-friendly access to the contents of the Effective database, allows the submission of compute jobs and provides documentation and supplementary data for specific methods of EffectiveDB. The EffectiveDB team appreciates your feedback on the new website. Prediction of microbial phenotypes based on comparative genomics. 43 1 4277 76681. 43 1 4277 876681.

effectivedb.org

Links | EffectiveDB

http://www.effectivedb.org/links

Dept of Microbiology and Ecosystem Science. Prediction of Type III secreted proteins. Prediction of Type IV secreted proteins. Proteins involved in bacterial secretion systems. EffectiveELD 5.1: Eukaryotic-like domain prediction upgraded to Pfam 29. New release 5.0 of Eukaryotic-like domains finished. EffectiveDB-updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Prediction of microbial phenotypes based on comparative genomics.

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...

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GenSkew - visualization of nucleotide skew in genome sequences

GenSkew: Genomic nucleotide skew application. GenSkew is an application for computing and plotting nucleotide skew data. It was developed at the TU Munich, Genome oriented bioinformatics. During a 2 weeks-practical in bioinformatics programming by the students Miroslava Edelstein, Florian Gehrke, Sonja Hopf, Andre Jehl and Annahita Oswald, supervised by Thomas Rattei. Since 2010, GenSkew is maintained by the Department of Computational Systems Biology of the University of Vienna. DNA sequence file in FAS...

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