Overview

Genome browsers are extremely useful to represent genomic data, such as SNPs, gene expression, methylation, etc., on the genomic context. Different genome browsers on the web are available, being the most popular the Ensembl and the UCSC. However, with the continuous increase in the available genomic data and metadata along with the limitations derived from extensive data traffic imposed by client/server architecture, such browsers become inevitably slower. Genome Maps is based on the new HTML5 standards, including SVG and Javascript and runs 100% in the in the modern web browsers (in a philosophy similar to Google). This makes unnecessary the installation of any Flash plug-in, Java Applet or any other technology and results in a fast and dynamic response to user requests. Genome Maps allows real-time navigation along chromosomes and karyotypes, representing different types of data over many types of genomic information. There are numerous pre-configured tracks such as genes, transcripts, SNPs, mutations, miRNA targets, conserved regions, TFBS, etc. There are also several DAS sources available, but new ones can easily be added to the system.

Genomic data in different standard formats (GFF, BED, VCF) can straightforwardly be imported and displayed on the viewer. Resulting images can be exported in the standard graphic formats PNG and JPEG. The zoom level can be changed to have different views at different details (from the highest level at nucleotide resolution to lowest levels). Since gene properties are available the search function can exploit them giving a wealth of search possibilities from genes, transcripts, exons, etc., and their variants, to functional (GO, Interpro, Reactome) and regulatory (Jaspar TFBSs or miRNA targets). Setting the cursor over any element in the view pops up a small window with all the relevant information on that element.

Currently, only Homo sapiens, Mus musculus, Rattus norvegicus, C. elegans and Danio rerio species are included, but soon more species will be available.

Users can also upload to Genome Maps their own gene expression and genotyping data to visualize them and run some basic analysis. New data and analysis will be available in the near future. Genome Maps works also like an API and can be used by developers. Integrating a fully operating version of Genome Maps in any web application is as easy as including in the HTML the two lines below:

   var genomeMaps = new GenomeMaps();
   genomeMaps.draw()

Genome Maps represents a new generation of efficient genome viewers in which many heterogeneous genomic data and metadata can be integrated and displayed in the Web browser with no need of any installation or update.

Genome Maps is available at: http://www.genomemaps.org/

Members

Head of the Department: Joaquin Dopazo
Project Manager: Ignacio Medina
Bioinformatician: Ignacio Medina, Luz Garcia, Marta Bleda
Software Developer: Alejandro de MarĂ­a, Francisco Salavert