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We think that being researchers we can design more useful tools and services for researchers. Besides, we are the first testers of our new developments and innovative services.


As a proof of our comittment to R&D Era7 funds the Era7 Bioinformatics Research Unit, named Oh no sequences! formed by a multidisciplinary team. We could say we love bioinformatics, genomics and category theory.


Oh no sequences! main projects

(check Oh no sequences! site or contact us for more information)



Bio4j is a bioinformatics graph based DB including most data available in UniProt (SwissProt + Trembl) plus Gene Ontology (GO) and UniRef (50,90,100). (Manuscript in preparation)



Using BG7 (manuscript submitted) we released a draft annotation of the first strain of the E Coli EHEC O104 causing the last European outbreak. Our BG7 annotation for this first outbreak strain was publicly available the next day of having the first assembly available. And we also set up a public Github repository allowing people around the world to share their own data and analysis in what was later called 'E. coli O104:H4 Genome Analysis Crowdsourcing'. In this repository you can access many data relative to this outbreak:


BG7 annotation system is an open source project in continuous improvement. If you want to know how BG7 works look at:


BG7 is mainly funded by era7 bioinformatics, with partial support from:


Proyecto INNPACTO | brachVac


Nº Expediente: IPT-2011-0735-010000


Título del Proyecto: “Desarrollo de una vacuna “global” frente a Brachyspira hyodysenteriae y Brachyspira pilosicoli mediante análisis pan-genómico estructural y funcional combinado con tecnologías de producción de proteínas recombinantes”




  • MG7:a new cloud computing system for massive analysis of reads from metagenomics samples


Right now we are working on a new system for analysis of metagenomics reads based on the use of cloud computing for the parallel computation of the BLAST similarity in which the inference of function and the assignation of taxonomical origin are based . A special peculiarity of MG7 system is the utilization of a non relational model database. MG7 uses Neo4j database to hold the results of the analysis and to facilitate the querying and the access to the data of the analysis.

The assignation of a read to a taxon in MG7 system is carried out based on the paradigm of the Lowest Common Ancestor.



Oh no sequences! main research lines



We actively participate as a research group in scientific networks, discussion forums and collaborative projects.

And as any other research group, we are interested in collaborating in research projects and in participating in EU projects. Feel free to contact us.





Phagosomes induced by cytokines function as anti-listeria vaccines: a novel role for functional compartmentalization of STAT-1 and cathepsin-D.

Carrasco-Marín E, Rodriguez-Del Rio E, Frande-Cabanes E, Tobes R, Pareja E, Lecea-Cuello MJ, Ruiz-Sáez M, Madrazo-Toca F, Hölscher C, Alvarez-Dominguez C. J Biol Chem. 2012 Feb 15

The intact structural form of LLO in endosomes cannot protect against listeriosis.

Rodriguez-Del Rio E, Frande-Cabanes E, Tobes R, Pareja E, Lecea-Cuello MJ, Ruiz-Sáez M, Carrasco-Marín E, Alvarez-Dominguez C.Int J Biochem Mol Biol. 2011;2(3):207-18. Epub 2011 Jul 15.
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.

Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R; E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium. N Engl J Med. 2011 Aug 25;365(8):718-24. Epub 2011 Jul 27. (**Marina Manrique from Era7 is a member of the Genome Analysis Crowd-Sourcing Consortium)

The innate immunity role of cathepsin-D is linked to Trp-491 and Trp-492 residues of listeriolysin O. 
Carrasco-Marín E, Madrazo-Toca F, de Los Toyos JR, Cacho-Alonso E, Tobes R, Pareja E, Paradela A, Albar JP, Chen W, Gomez-Lopez MT, Alvarez-Dominguez C.
Mol Microbiol. 2009 Apr 6. 
Characterization of a Listeria monocytogenes protein interfering with Rab5a. 
Alvarez-Dominguez C, Madrazo-Toca F, Fernandez-Prieto L, Vandekerckhove J, Pareja E, Tobes R, Gomez-Lopez MT, Del Cerro-Vadillo E, Fresno M, Leyva-Cobián F, Carrasco-Marín E.
Traffic. 2008 Mar;9(3):325-37. 
Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9. 
Magnusson M, Tobes R, Sancho J, Pareja E.
J Immunol. 2007 Jul 1;179(1):31-5.
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. 
Tobes R, Pareja E.
BMC Genomics. 2006 Mar 24;7:62. Review.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. 
Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
BMC Microbiol. 2006 Mar 15;6:29.
Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation. 
Tobes R, Pareja E.
Res Microbiol. 2005 Apr;156(3):424-33. Epub 2005 Jan 28. 
Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. 
Yuste L, Hervás AB, Canosa I, Tobes R, Jiménez JI, Nogales J, Pérez-Pérez MM, Santero E, Díaz E, Ramos JL, de Lorenzo V, Rojo F. 
Environ Microbiol. 2006 Jan;8(1):165-77 
The TetR family of transcriptional repressors. 
Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R. 
Microbiol Mol Biol Rev. 2005 Jun;69(2):326-56 
REP code: defining bacterial identity in extragenic space. 
Tobes R, Ramos JL. 
Environ Microbiol. 2005 Feb;7(2):225-8. 
BacTregulators: a database of transcriptional regulators in bacteria and archaea. 
Martínez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R. 
Bioinformatics. 2004 Nov 1;20(16):2787-91 
Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01. 
Martínez-Bueno MA, Tobes R, Rey M, Ramos JL. 
Environ Microbiol. 2002 Dec;4(12):842-55. 
Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. 
Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marqués S. 
Nucleic Acids Res. 2002 Apr 15;30(8):1826-33.
AraC-XylS database: a family of positive transcriptional regulators in bacteria. 
Tobes R, Ramos JL. 
Nucleic Acids Res. 2002 Jan 1;30(1):318-21.