ZMap

A Desktop Genome Browser.

ZMap is a genome browser written in C with the aim of providing fast access to high volume data. Data may be requested from a variety of disparate sources in parallel and cached locally allowing new tracks to be loaded or the view of current data adjusted without delay. Multiple views of the data may be presented and tracks configured for different levels of detail. ZMap interfaces seamlessly to the Seqtools package and forms part of the Otterlace genome annotation system used by the HAVANA group at the Wellcome Trust Sanger Institute.

ZMap may also be used as a standalone browser taking data either from external soruces or from simple GFF files held locally.

[Genome Research Limited]

Information

ZMap features

  • genomic and feature data cached locally
  • multiple views of the same or different regions
  • configurable display of tracks (show/hide)
  • compact, information rich display of alignments and other features
  • configurable display styles for different type of features
  • traffic light markers for incomplete homolgies
  • non-concensus splice markers
  • highlight evidence for transcripts
  • masking of EST's to remove duplication
  • automatic point and click interface to Blixem
  • 3-Frame Translation (3FT) of genomic DNA
  • highlight of 3FT showing frame shifts and split codons
  • powerful feature search functions
  • request and display selected sub-sequences ('request from mark')
  • navigator pane showing overall view of loaded sequence, allowing zoom to locus and visual scroll
  • pfetch selected features

Background

ZMap is derived from FMap which was originally written as part of the AceDB genome database system. Version 0.1 involved an extensive re-write to take advantage of modern GUI toolkits and to separate them from AceDB to form this independent ZMap package. It can be used independently or with any other tool that outputs data in a suitable format - the currently supported file format is GFF v2 (GFF v3 will be supported in the near future).

Supported platforms

Currently supported platforms are Linux and Mac OS X (Intel).

Licence

ZMap is free software and is distributed under the terms of the GNU General Public License.

Screenshots

ZMap - whole sequence

ZMap - whole sequence

zoom

ZMap - multiple views

ZMap - multiple views

zoom

ZMap navigator pane

ZMap navigator pane

zoom

Column configuration

Column configuration

zoom

Request features from marked region

Request features from marked region

zoom

ZMap - feature menu

ZMap - feature menu

zoom

ZMap - search and results

ZMap - search and results

zoom

Homology and non-concensus splice markers

Homology and non-concensus splice markers

zoom

ZMap - 3-frame translation showing frame shifts

ZMap - 3-frame translation showing frame shifts

zoom

Download

Note that the SeqTools package provides some optional tools that can be called from within ZMap to give a more detailed nucleotide-level view of alignments. It is not required to run ZMap, and it can be installed at a later date if you don't want to install it initially.

Production release

This is the recommended release for most users. It is well-tested, stable and supported code.

The latest version is 1.0.0, created on Tue Sep 30 12:28:11 BST 2014:
seqtools-4.29.tar.gz
zmap-1.0.0.tar.gz

Development build

Reasonably stable development code, which contains most of the latest features.

The latest version is 1.0.0-366-g5fe4a50, created on Fri Oct 17 15:53:01 BST 2014:
seqtools-4.29-4-gd795.tar.gz
zmap-1.0.0-366-g5fe4a50.tar.gz

Overnight build

Experimental code; not guaranteed to be stable (or even to compile). Should only be used if you require the very latest changes.

The latest version is 1.0.0-372-g81bd042, created on Tue Oct 21 23:21:40 BST 2014:
seqtools-4.29-4-gd795.tar.gz
zmap-1.0.0-372-g81bd042.tar.gz

Installation

Prerequisites

The ZMap package requires GTK+ version 2.18.6 and GLib version 2.22.4 or later and libg2 and libgd to be installed on your machine.

Note that the SeqTools package provides some optional tools that can be called from within ZMap to show a detailed nucleotide-level view of alignments. This package is not a prerequisite and ZMap will run fine without it. SeqTools can be installed at a later date if you don't want to install it initially.

Installation

To install on either Linux or Mac OS X:

  • Download the source code from the Download page. The downloaded file will be a tar file named zmap-XXX.tar.gz, where XXX is the version number.
  • Unpack the tar file, e.g. by typing the following in a terminal:
    tar -xf zmap-XXX.tar.gz
    
    This will create a directory called zmap-XXX.
  • To install the package in the default location (usually /usr/bin), open a terminal in the zmap-XXX directory and type the following commands:
    ./configure 
    make
    make install

Tips

  • You may need to run make install using sudo if you do not have root privileges, i.e.:
    sudo make install
    
  • Alternatively, to install to a different location (e.g. one not requiring root privileges), use the --prefix argument when you run ./configure. For example, the following command would set the install location to foo/bar in your home directory:
    ./configure --prefix=~/foo/bar
    

For more details about installation, see the README file in the source code.

An example: installing ZMap on a standard Linux release (Ubuntu 10.10)

As installing ZMap from the source distribution requires your PC to have some development packages loaded it may be necessary to install other software first. Each Linux system may differ in what is included by default and the following is an example only - these are the packages we had to install to compile ZMap on this system. When you run ./configure this may fail due to missing packages and it will be necessary to load these before trying again; this is most easily done (on Ubuntu) using synaptic (available from the System/Administration menu).

Install pre-requisites

Using synaptic, check that the following packages are installed: libgtk-2.0-dev, libglib2.0-dev, libreadline6-dev, libg2-dev, libgd2-xpm-dev, libcurl4-gnutils-dev. NOTE we list all these dependencies here together, but we had to run synaptic and ./configure several times to find them all.

Documentation

Getting started

Run zmap --help to see usage information. ZMap can be run with a GFF file on the command-line (development version only at the moment) or with a configuration file that sets up the data sources. A sample GFF file is provided in the examples directory (development version only); to try it, run ZMap like this:

zmap examples/features.gff

User manuals

There is a user manual (thanks to Charles Steward) available here.

Help pages

Help pages are installed along with ZMap and can be accessed from the Help menu. There will be a link to the user manual from the help pages, if one is available.

Publications

Contact

ZMap is maintained by the Annotools team at the Sanger Institute.

* quick link - http://q.sanger.ac.uk/1neddsuq