Taverna: a tool for building and running workflows of services
TLDR
Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services, to perform a range of different analyses, such as sequence analysis and genome annotation.Abstract:
Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/.read more
Citations
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Unipro UGENE
TL;DR: Unipro UGENE integrates widely used bioinformatics tools within a common user interface and provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures.
Journal ArticleDOI
A new bioinformatics analysis tools framework at EMBL–EBI
Mickael Goujon,Hamish McWilliam,Weizhong Li,Franck Valentin,Silvano Squizzato,Juri Paern,Rodrigo Lopez +6 more
TL;DR: A new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface is presented.
Journal ArticleDOI
Analysis Tool Web Services from the EMBL-EBI
Hamish McWilliam,Weizhong Li,Mahmut Uludag,Silvano Squizzato,Youngmi Park,Nicola Buso,Andrew Peter Cowley,Rodrigo Lopez +7 more
TL;DR: Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces, which allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows.
Journal ArticleDOI
The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
David Swarbreck,Christopher Wilks,Philippe Lamesch,Tanya Z. Berardini,Margarita Garcia-Hernandez,Hartmut Foerster,Donghui Li,Tom Meyer,Robert J. Muller,Larry Ploetz,Amie Radenbaugh,Shanker Singh,Vanessa Swing,Christophe Tissier,Peifen Zhang,Eva Huala +15 more
TL;DR: A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models).
Journal ArticleDOI
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows
Maria D. Paraskevopoulou,Georgios Georgakilas,Nikos Kostoulas,Ioannis S. Vlachos,Thanasis Vergoulis,Martin Reczko,Christos Filippidis,Theodore Dalamagas,Artemis G. Hatzigeorgiou +8 more
TL;DR: DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA- microT-CDS, which has been updated to incorporate miRBase version 18 and Ensembl version 69.
References
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