Genome Maps, a new generation genome browser

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

[1]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[2]  Qunfeng Dong,et al.  WebGBrowse - a web server for GBrowse , 2009, Bioinform..

[3]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[4]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[5]  Antony V. Cox,et al.  The Ensembl Web site: mechanics of a genome browser. , 2004, Genome research.

[6]  M. Cline,et al.  Understanding genome browsing , 2009, Nature Biotechnology.

[7]  Marta Bleda,et al.  CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources , 2012, Nucleic Acids Res..

[8]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[9]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[10]  M. Bhagwat,et al.  Searching NCBI's dbSNP Database , 2010, Current protocols in bioinformatics.

[11]  David J. Arenillas,et al.  JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles , 2009, Nucleic Acids Res..

[12]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[13]  Xiaokun Li,et al.  MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation , 2010, Nucleic Acids Res..

[14]  Maureen J Donlin,et al.  Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.

[15]  Masaru Tomita,et al.  Genome Projector: zoomable genome map with multiple views , 2009, BMC Bioinformatics.

[16]  Julien Lajugie,et al.  GenPlay, a multipurpose genome analyzer and browser , 2011, Bioinform..

[17]  Maureen J Donlin,et al.  Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.

[18]  Sharon R Grossman,et al.  Integrating common and rare genetic variation in diverse human populations , 2010, Nature.

[19]  Michal J. Okoniewski,et al.  X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis , 2007, Nucleic Acids Res..

[20]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[21]  Tim J. P. Hubbard,et al.  Dalliance: interactive genome viewing on the web , 2011, Bioinform..

[22]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[23]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[24]  Philip Jones,et al.  The InterPro BioMart: federated query and web service access to the InterPro Resource , 2011, Database J. Biol. Databases Curation.

[25]  Gabor T. Marth,et al.  Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web , 2013, Bioinform..

[26]  Qunfeng Dong,et al.  xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features , 2006, Genome Biology.

[27]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[28]  Cristina Y. González,et al.  VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing , 2012, Nucleic Acids Res..