Spain-based Era7 Bioinformatics plans to open an office in Boston within a few weeks so that it can offer its cloud-based annotation services — focused primarily on bacterial genomes and metagenomes — to US customers.
The new subsidiary will add to the company's existing offices in Madrid and Granada, and will also increase its headcount as Era7 plans to hire additional staff to manage its newest shop, Eduardo Pareja, the company's CEO, told BioInform this week.
The 14-person company, which officially opened its doors about five years ago, helps customers design their sequencing projects, providing guidance on setting project goals, selecting appropriate sequencing technologies, and finding sequence providers. It also provides analysis and annotation of the results as well as data management software, Pareja said.
Era7's business model "is not to sell software licenses," he said. Rather, it is to provide "service[s] [to] the customer or to help the customer to integrate our open source software into their own IT infrastructure."
One of its open source projects, Bio4j, is a database that contains information from resources like UniProt and UniRef and is based on Neo4j — an open source NOSQL graph database. Bio4j provides a framework for protein-related information querying and management. It was developed by Era7's R&D arm, which goes by the name Oh No Sequences.
Pareja said that the company chooses to make its internal pipelines available under an open source model because it is "convinced" that this is the only way it can to keep up with the rapidly evolving face of bioinformatics and integrate with new tools as they develop.
Era7 offers two cloud-based services specifically for next-generation sequencing data — BG7annotation for bacterial genomes and MG7 metagenomics for annotating metagenomics data.
BG7 is a bacterial genome annotation system that offers gene prediction integrated with functional annotation using resources such as the Gene Ontology. It detects insertions, deletions, or substitutions and predicts open reading frames and annotates them based on similarities with proteins in UniProt.
For its part, the MG7 service provides annotation for large quantities of sequences as well as information about biodiversity and function.
The company also offers RNA-seq data analysis for both model and non-model organisms as well as exome analysis for model organisms, Pareja explained.
Analysis services offered for RNA-seq data include functional annotation, gene expression quantification, differential expression analysis, and de novo characterization of transcriptomes, among other features.
Exome services include read quality analysis, read mapping to reference genomes using the Burrows-Wheeler aligner, realignment and recalibration with the Genome Analysis Toolkit; and detection of variants, among other offerings.
Era7 targets its RNA-seq and exome services primarily at Spain-based researchers, however, since there are numerous software vendors that offer these analysis services outside the country and Era7 wants to differentiate itself from companies that offer services in that space, Pareja said.
Furthermore, "we are more skilled in bacterial genomics and metagenomics," he said, and as such the company will primarily promote its bacterial analysis and annotation services to US customers, although it will offer RNA-seq and exome analysis services to those groups if they request it.
Pricing for Era7’s analysis offerings are determined on a per-project basis, Pareja said.
The company’s primary market include scientists in research groups and institutions, universities, hospital clinical microbiology laboratories, biotechnology and pharmaceutical companies, sequencing service providers, bioinformatics facilities, and contract research organizations.
It expects that its microbial annotation services will appeal to small research groups that don't want to deal with the bioinformatics aspects of their research themselves as well as medium and larger centers that are looking to incorporate Era7's informatics pipelines into their existing infrastructure, Pareja said.
Earlier this year, Era7 was selected to work with the Hospital Universitario La Paz Research Institute in order to assemble and annotate sequences from whole-genome sequencing of three antibiotic-resistant strains of the bacterium Klebsiella pneunomiae sequenced on a Roche 454 GS FLX+ system.
In February, the company was one of several firms tapped by Pacific Biosciences to provide informatics analysis options to customers of its Single Molecule Real Time sequencer (BI 2/17/2012).