Genome Maps Overview

Introduction

Genome Maps has been designed to provide the scientific community with a new, fast and plugin-free visualization tool. Genome Maps allows real-time navigation along chromosomes and karyotypes of many species, 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 or TFBSs. There are also several DAS sources available, but new ones can easily be added to the system. Unlike other genome browsers, Genome Maps allows users can import their own experimental data (genotype, expression, variant call, etc) and display it as a new track.

Genome Maps is not only a new genome viewer, but an analysis tool a plugin-oriented tool aimed to bioinformatic developers and users.

Genome Maps currently supports the following functionalities:

  • Different species supported: Homo sapiens, Mus musculus and Danio rerio among others
  • Genome browsing using different zoom levels and positioning using coordinates, chromosome, karyotype or identifier.
  • Visualization of different biological information: core (gene, transcripts, sequence, etc), variation (SNPs) and regulatory features (miRNA targets, transcription factor binding sites, polymerase binding, open chromatin regions, etc.), DAS sources (CRG, cosmic mutations, etc.)
  • Information widgets containing extra information related with the feature.
  • Visualization of users file. Accepted formats: VCF, GFF, BED and expression matrix.
  • Export an image of the current visualization.

Goals

Genome Maps aims to provide to the community with an fast and modern Genome browser that exploits the benefits of current WEB technologies such as RESTful WEB services and HTML5.

Features

Browser features

  • The web interface contains the conventional elements of a genome browser.
  • Genome annotations are represented against the corresponding reference genome, with an overhead navigation bar giving a visual indication of chromosome position.
  • Navigation is done by dragging the display left or right, which produces a smooth panning effect.
  • The zoom level can be changed to have different views at different details (from the highest level at nucleotide resolution to lowest levels).
  • The view configuration can easily be changed through a menu that allows adding or removing different tracks with different types of genomic information (see below).
  • Many gene properties are available for genes, transcripts and exons, which include their different types of variations, functional properties (GO, Interpro, Reactome) and regulatory elements (Jaspar TFBSs or miRNA targets).
  • A DAS client has also been implemented and users can also add tracks with preconfigured DAS servers or any other DAS server.
  • If the cursor is set over any element in the view, a small window pops up with all the relevant information on that element.
  • Some elements show a rich info window when they are clicked.
  • For genes and transcripts If 3D structures are also available, these are also represented for genes.
  • There is also a search function that can use all the information mentioned above, giving a wealth of search possibilities.
  • Genes and transcripts colours are displayed according to their biotype meanwhile for SNPs the consequence type is used, gene and SNPs legends are showed at the bottom part.

Detailed browser features

Biological features

Detailed biological features

Tutorials

In this section you will find some interesting tutorial about how to use Genome Maps

  • Basic navigation and searching for a gene or feature
  • Using URL Query Parameters
  • Howto add DAS source
  • Importing a local or remote file into Genome Maps
  • Downloading and integrating Genome Maps into your project or resources
  • Developing new tracks for custom data
  • many more

Just click in this link for more information.

Technology and architecture

sencha, jquery, html5, SVG, REStful web services, architectura, ...

The user navigates along the genome and request different types of information. This produces queries to the remote server that through a RESTful Web Service manages the queries to the database and serves the requested information. DAS servers can also serve information on Genome Maps. Users can also visualize different types of data (in different formats such as VCF, BED or GFF) on the genomic context.

Server backened

Follow this TUTORIAL to learn how to integrate and configure a Genome Maps.

Releases and downloads

Genome Maps is released under the terms of GPLv2 license. The current stable version of Genome Maps is v2.2.1, released September 2012, this is a minor relased with a few bugs fixed, details at:

Release note v2.2.1

More information about older releases: All release notes

You can download latest version of Genome Maps code at:

genome-maps-v3.0.0-src.tar.gz

Just extract the files and open with a web browser the genomemaps.html file located in genome-maps folder, or put them in your http server folder.

genome-maps-v2.1.3-src.tar.gz (1.8 MB) Francisco Salavert, 09/27/2012 06:18 pm

genome-maps-v2.1.5-src.tar.gz (1.8 MB) Francisco Salavert, 10/08/2012 12:50 pm

genome-maps-v2.2.1-src.tar.gz (1.8 MB) Francisco Salavert, 11/16/2012 03:53 pm

genome-maps-v3.0.0-src.tar.gz (1.8 MB) Francisco Salavert, 12/28/2012 03:57 pm