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Scipio is used for the retrieval of the genome sequence corresponding to a protein query. The tool does not require any annotation data, and is able to correctly identify the gene even if this is spread on several genome contigs and contains mismatches and frameshifts. Because of its post-processing capabilities, Scipio is not only able to correctly identify the gene in the genome corresponding to the protein query but also to correctly identify the homologous genes in the genomes of closely related organis

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Scipio | Home | webscipio.org Reviews

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Scipio is used for the retrieval of the genome sequence corresponding to a protein query. The tool does not require any annotation data, and is able to correctly identify the gene even if this is spread on several genome contigs and contains mismatches and frameshifts. Because of its post-processing capabilities, Scipio is not only able to correctly identify the gene in the genome corresponding to the protein query but also to correctly identify the homologous genes in the genomes of closely related organis

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1 scipio

2 webscipio

3 gene prediction

4 gene

5 splice site

6 genome

7 taxonomy

8 gÃ¶ttingen

9 max-planck-institute

10 manual sequence annotation

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webscipio,upload result file,genomes,team,webservice,download,welcome to webscipio,publications,bmc bioinformatics,bmc research notes,bmc genomics,newest genomes,taxonomy,contigs,38 gc content,show up to,feedback,restrictions and licence,impressum

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Scipio | Home | webscipio.org Reviews

https://webscipio.org

Scipio is used for the retrieval of the genome sequence corresponding to a protein query. The tool does not require any annotation data, and is able to correctly identify the gene even if this is spread on several genome contigs and contains mismatches and frameshifts. Because of its post-processing capabilities, Scipio is not only able to correctly identify the gene in the genome corresponding to the protein query but also to correctly identify the homologous genes in the genomes of closely related organis

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webscipio.org

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Scipio | Download

http://www.webscipio.org/webscipio/download_scipio

Using WebScipio and Scipio by non-academics requires permission. WebScipio and Scipio may be obtained upon request and used under a GNU General Public License. If you use Scipio for your research, please cite:. O Keller, F. Odronitz, M. Stanke, M. Kollmar and S. Waack (2008). Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. Download the latest version of the Scipio command line tool:. Scipio Version 1.4. Hence, the ol...

2

Scipio | Help | WebScipio

http://www.webscipio.org/help

Download this help page as PDF. Selecting a species and a genome dataset. Entering the protein query. Setting Scipio's search options. Scaling in gene pictures. To obtain the gene structure corresponding to a certain protein query, first select a species and a genome dataset, then enter your protein query, optionally adjust Scipio's settings, and finally start Scipio. Selecting a species and a genome dataset. Entering the protein query. Setting Scipio's search options. Sometimes, there are gene duplicate...

3

Scipio | Team

http://www.webscipio.org/webscipio/team

Dr Martin Kollmar, PI. Prof Dr. Stephan Waack, PI. October 2006 - January 2011. October 2006 - March 2009. M Sc Holger Pillmann. July 2007 - July 2009. 169; Scipio Team 2016.

4

Scipio | WebService

http://www.webscipio.org/webscipio/web_service

WebScipio RESTful Web Service. You can access the functionality of WebScipio from within any software program by using the web service API. To illustrate the process, we show a transcript of a session in Ruby, which can easily be adapted to your programming language:. Lines starting with a number in brackets are user input. Lines starting with "= " are responses from the server. Url = URI.parse("http:/ www.webscipio.org/api searches"). Post parameters = {'search species' = 'true', 'query' = 'drosophila'}.

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cymobase.org

cymobase | help

http://www.cymobase.org/cymobase/help

How to use Cymobase's search modules. Search by author,. All species results will be listed under the reference scientific name (according to the NCBI taxonomy browser). Thus anamorphs will be listed under their teleomorph names (e.g. if you are searching for Fusarium verticillioides. The main entry will be Gibberella moniliformis. Citing F. verticillioides. As anamorph) and the same accounts for alternative scientific and common names. Species Names Search Module. Protein Classes Search Module. The Taxo...

diark.org

diArk | links

http://www.diark.org/diark/links

Links to other relevant information. Information about Sequencing Projects. The Genome 10K project aims to assemble a genomic zoo a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus.". The 1000 plants (oneKP or 1KP) initiative is a public-private partnership generating large scale gene sequence information for 1000 different species of plants.". I5k Insect and other Arthropod Genome Sequencing Initiative. The ISC has establishe...

diark.org

diArk | team

http://www.diark.org/diark/team

Dr Martin Kollmar, PI. April 2009 - March 2013. Aug 2006 - June 2011. Dipl Biol. Sebastian Becker. Feb 2007 - Jan. 2009. May 2005 - Feb. 2009. DiArk 3.0 Content. 2 Clicks for more privacy: You have to click the top icon to enable the Facebook Like, the Twitter, or the Google button. 169; diArk 3.0 Team 2006-2016 Impressum.

diark.org

diArk | news

http://www.diark.org/diark/news

2011-09-28 - New diArk publication. We proudly present the new diArk paper. It describes the newest features of diArk and the available data. Furthermore, it compares diArk to related databases and explains, why you should use diArk. B Hammesfahr, F. Odronitz, M. Hellkamp and M. Kollmar (2011). DiArk 3.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data. 2011-03-30 - New welcome page. 2011-03-28 - New function: Sharing your search. 2010-09-07 - New functions and changes.

diark.org

diArk | help

http://www.diark.org/diark/help

How to use diArk's search modules. Information provided by diArk's result views. How to use diArk's search modules. Search by author,. All species results will be listed under the reference scientific name (according to the NCBI taxonomy browser). Thus anamorphs will be listed under their teleomorph names (e.g. if you are searching for Fusarium verticillioides. The main entry will be Gibberella moniliformis. Citing F. verticillioides. Species Names Search Module. The Taxonomy Search Module offers tables ...

diark.org

diArk | statistics

http://www.diark.org/diark/statistics

The statistic graphs on this page are based on the newest data available at diArk. This means, if there is a database update, the graphs will be generated as well (updated: 2016-08-15). DiArk 3.0 Content. 2 Clicks for more privacy: You have to click the top icon to enable the Facebook Like, the Twitter, or the Google button. 169; diArk 3.0 Team 2006-2016 Impressum.

diark.org

diArk | species_list

http://www.diark.org/diark/species_list/homo%20sapiens

Opisthokonta Metazoa Eumetazoa . . . Hominidae Homininae Homo ]. Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Deuterostomia Chordata Craniata Vertebrata Gnathostomata Teleostomi Euteleostomi Sarcopterygii Dipnotetrapodomorpha Tetrapoda Amniota Mammalia Theria Eutheria Boreoeutheria Euarchontoglires Primates Haplorrhini Simiiformes Catarrhini Hominoidea Hominidae Homininae Homo. Go to NCBI Taxonomy (9606). GenBank - NIH genetic sequence database: GenBank species TBLASTN. Proc Natl Acad Sci U S A.

motorprotein.de

motorprotein | group | group leader

http://www.motorprotein.de/group.html

Since Oct. 2007. Faculty member of GGNB. Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences. Venia legendi in Strukturchemie. Umwandlung chemischer Energie in Bewegung: Struktur- und Sequenzbasierte Untersuchungen von Motor-Proteinen". Faculty of Chemistry, Georg-August-Universität Göttingen. Department of NMR Based Structural Biology. Max-Planck Institute for Biophysical Chemistry, Göttingen. March 1999 Feb. 2002. June 1998 March 1999. Feb 1997 July 1997. Oct 1995 May 1998.

motorprotein.de

motorprotein | funding

http://www.motorprotein.de/funding.html

We are very greatful to the Department of NMR-based Structural Biology at the Max-Planck-Institute for Biophysical Chemistry for providing the infrastructure for our work. Deutsche Forschungsgemeinschaft Research Grants. KO 2251/13-1 (since 2013). Deutsche Forschungsgemeinschaft Research Grants. KO 2251/5-1 (together with Prof. M. Schliwa and Prof. J. Parsch, 2007-2010). KO 2251/3-1, KO 2251/3-2, KO 2251/3-3 (2006-2014). Together with Prof. T. Carlomagno, Prof. M. Baldus and.

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Web Science and the Mind

Web Science and the Mind. Sunday, 8 June 2014. Web Science: It's All in the Mind. University of Southampton, Electronics and Computer Science. Berners-Lee, T., Hall, W., Hendler, J., Shadbolt, N., and Weitzner, D. (2006). Creating a Science of the Web. Berners-Lee, T., Hall, W., Hendler, J. A., O'Hara, K., Shadbolt, N., and Weitzner, D. J. (2006). A framework for web science. Foundations and trends in Web Science. Communications of the ACM. Foundations and Trends in Web Science. Towards a Global Brain:.

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WebScio | Blueprints for the Web

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Scipio | Home

It is very time-consuming to always provide the latest genome assemblies. Thus, if you want Scipio/WebScipio to be continuously updated and its functionality extended in the future please properly cite the respective parts of the software! If you use Scipio (command-line version), please cite:. O Keller, F. Odronitz, M. Stanke, M. Kollmar and S. Waack (2008). Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. Opisthokon...

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