Eduardo Pareja-Tobes

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Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory proteins and the regulatory DNA signals located in extragenic regions are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and(More)
BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected(More)
New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial(More)
Today's biology involves many times the use of different omics approaches , in particular, data and information from genomes and proteins are frequently difficult to integrate. In order to manage in an integrated way the information about complete genomes and proteomes in BG7 based projects we developed the Bio4J platform (www.bio4j.com). Bio4j is a(More)
Nowadays it is widely accepted that the bioinformatics data analysis is a r eal b ottleneck i n many r esearch act ivities r elated t o l ife s ciences. H igh-throughput t echnologies l ike N ext Generation S equencing (NGS) ha ve completely r eshaped t he bi ology a nd bi oinformatics l andscape. U ndoubtedly NGS has allowed important progress in many(More)
Identification and epidemiologic studies of pathogenic bacteria are mainly based on genotyping of a set of selected genes. The availability of Next Generation Sequencing technologies allows doing an exhaustive genotyping of the strains involved in outbreaks sequencing their whole genome. To have the sequences of the complete set of genes of a bacteria opens(More)
Bio4j (http://bio4j.com) is a high-performance cloud-enabled graph-based bi oinformatics da ta pl atform. I t i s one of t he first a nd most i mportant graph databases for biological data, specially designed to cope with and manage the huge amount of data brought by NGS technologies: it i ntegrates most data available in U niProt K B (SwissProt + Trembl),(More)
Methods: MG7 i s a n ope n s ource t ool i mplemented i n J ava a nd Scala, ba sed on c loud c omputing (Amazon W eb S ervices). The g raph da ta platform B io4j (www.bio4j.com) i s us ed f or r etrieving t axonomy r elated information, w hile N ispero (http://ohnosequences.com/nispero) i s used f or distributing and coordinating compute tasks. Results: MG7(More)
Next Generation Sequencing (NGS) has brought a revolution to the bioinformatics l andscape, de finitely r eshaping f ields s uch a s g enomics a nd transcriptomics, by o ffering sheer amounts of data about previously inaccessible d omains i n a c heap a nd s calable w ay. Thus bi ological da ta a nalysis d e-mands, more than ever, high performance computing(More)
As part of the Cambrian explosion of omics data, metagenomics brings to the table a specific, defining trait: its social essence. The meta prefix exerts its influence, with multitudes manifesting themselves everywhere; from samples to data analysis, from actors involved to (present and future) applications. Of these dimensions, data analysis is where needs(More)
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