EMBnet.journal

The Swedish EMBnet Node: AGM 2010 report

Nils-Einar Eriksson

Computing Department of Uppsala Biomedical Centre (BMC), Uppsala, Sweden

People working for EMBnet Sweden are Nils-Einar Eriksson (TM PC), Emil Lundberg, Martin

Norling (PR PC) and Erik Bongcam-Rudloff (EMBnet chairman 2003-2009).

Services

EMBnet Sweden has a web-site connected to several unique tools produced by members of EMBnet together with their associated researchers. EMBnet’s video conference system (Marratech) is located and managed at the Swedish node. Uppsala University is providing mail-list services for EMBnet. The lists are managed by node personnel. DNS master services for EMBnet are also provided by the Swedish node.

SeqScoring

The tool can be used to up-load your SNP- and indel- files from large re-sequencing projects, and get the data scored by conservation across species: www.seqscoring.net.

EVALLER

EVALLER™ is a web-tool wherein you can electronically test (e-Testing) a protein’s potential allergenicity/cross-reactivity based on its amino acid sequence (http://bioinformatics.bmc.uu.se/evaller.html).

MolMeth

MolMeth is a structured database that provides free access to methods used in molecular biology and molecular medicine. Submitted methods and contributions are subject to curation. www.molmeth.org.

RetroTector online

A web-based tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences: http://retrotector.neuro.uu.se/.

EMBnet Sweden has also being involved in the development of several bioinformatics packages and tools for the MacOSX platform:

• eBiotools: A collection of bioinformatics tools (>200): EMBOSS, Staden, T-coffee, ClustalW, and many others
• BioX: a graphical interface for eBiotools
• eBioKit: a server loaded with bioinformatics tools and databases, a solution for small and medium size research groups. The eBioKit is now used in more than 10 countries worldwide.

The node was one of the main organizers of the Next Generation Sequencing technologies workshop organized in Rome, November 2009, and of part II of the workshop in Bari-Italy, July 2010. (www.nextgensequencing.org).

Selection of Publications (2009-2010)

1. Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, Partners I, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G. The EMBRACE web service collection. Nucleic Acids Res. 2010 May 12. [Epub ahead of print]PMID: 20462862.
2. Markus Klint , Mikael Thollesson , Erik Bongcam-Rudloff , Svend Birkelund , Anders Nilsson and Bjorn Herrmann. Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis. BMC Microbiology 2010, 10:81doi: 10.1186/1471-2180-10-81 17 March 2010
3. Danika Bannasch, Amy Young, Jeffrey Myers, Katarina Truvé, Peter Dickinson, Jeffrey Gregg, Ryan Davis, Erik Bongcam-Rudloff, Matthew T. Webster, Kerstin Lindblad-Toh, and Niels Pedersen. Localization of Canine Brachycephaly Using an Across Breed Mapping Approach. PLoS One. 2010; 5(3): e9632. Published online 2010 March 10. doi: 10.1371/journal.pone.0009632
4. Heli Salminen-Mankonen, Jan-Eric Litton, Erik Bongcam-Rudloff, Kurt Zatloukal4 and Eero Vuorio. The Pan-European research infrastructure for Biobanking and Biomolecular Resources: managing resources for the future of biomedical research. EMBnet.News. 15.2. pp. 3-8. July 2009.
5. Álvaro Martínez Barrio, Erik Lagercrantz, Göran O Sperber, Jonas Blomberg, Erik Bongcam-Rudloff. Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX. BMC Bioinformatics. BMC Bioinformatics 2009, 10(Suppl 6):S18doi:10.1186/1471-2105-10-S6-S18
6. Domenica D’Elia , Andreas Gisel , Nils-Einar Eriksson , Sophia Kossida , Kimmo Mattila , Lubos Klucar and Erik Bongcam-Rudloff. The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community. BMC Bioinformatics. BMC Bioinformatics 2009, 10 (Suppl 6):S1doi:10.1186/1471-2105-10-S6-S1
7. R. P. Joosten, J. Salzemann, V. Bloch, H. Stockinger, A.-C. Berglund, C. Blanchet, E. Bongcam-Rudloff, C. Combet, A. L. Da Costa, G. Deleage, M. Diarena, R. Fabbretti, G. Fettahi, V. Flegel, A. Gisel, V. Kasam, T. Kervinen, E. Korpelainen, K. Mattila, M. Pagni, M. Reichstadt, V. Breton, I. J. Tickle and G. Vriend. PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J. Appl. Cryst. (2009). 42 [ doi:10.1107/S0021889809008784 ]
8. Sperber G, Lövgren A, Eriksson NE, Benachenhou F, Blomberg J. RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S4
9. Álvaro Martínez Barrio, Marie Ekjerlund, Göran O Sperber, Jonas Blomberg, Erik Bongcam-Rudloff and Göran Andersson. In silico analysis of the dog genome identifies Canine Endogenous Retroviruses (CfERVs). Frontiers of Retrovirology: Complex retroviruses, retroelements and their hosts Montpellier, France. 21-23 September 2009. Retrovirology 2009, 6(Suppl 2):P7doi:10.1186/1742-4690-6-S2-P7
10. David E. Gloriam, Sandra Orchard, Daniela Bertinetti, Erik Bjorling, Erik Bongcam-Rudloff, Julie Bourbeillon, Andrew R. Bradbury, Antoine de Daruvar, Stefan Dubel, Roanld Frank, Toby J. Gibson, Niall Haslam, Friedrich W. Herberg, Tara Hiltke, Jorg D. Hoheisel, Samuel Kerrien, Manfred Koegl, Zoltan Konthur, Bernhard Korn, Ulf Landegren, Silvere van der Maarel, Luisa Montecchi-Palazzi, Sandrine Palcy, Henry Rodriguez, Sonja Schweinsberg, Volker Sievert, Oda Stoevesandt, Michael J. Taussig, Mathias Uhlen, and Christer Wingren. A community standard format for the representation of protein affinity reagents. Molecular and Cellular Proteomics. August 2009.