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

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  • 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
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ZMap - multiple views

ZMap - multiple views
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ZMap navigator pane

ZMap navigator pane
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Column configuration

Column configuration
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Request features from marked region

Request features from marked region
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ZMap - feature menu

ZMap - feature menu
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ZMap - search and results

ZMap - search and results
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Homology and non-concensus splice markers

Homology and non-concensus splice markers
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ZMap - 3-frame translation showing frame shifts

ZMap - 3-frame translation showing frame shifts
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Download

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.

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

  • The above assumes that you have libACEConn installed; if not then follow a similar procedure with libACEConn - download the tar file, unpack it, configure and make.
  • 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.

Unpack and build libACEConn

(We assume that you have already downloaded the tar file by clicking on the link on the download tab).

Unpack the source code: 

mkdir zmap 
cd zmap 
tar -xf ~/Downloads/libAceConn-0-0-1.tar.gz

Compile it: 

cd libAceConn-0-0-1
./configure
make

Install this where ZMap can find it: 

sudo make install
cd ..
Unpack and build ZMap
tar -xf ~/Downloads/zmap-0-2-0.tar.gz

cd zmap-0-2-0
./configure
 make

This will leave a copy of ZMap in this directory and you can link to this or copy it to your bin directory or install it as normal: 

sudo make install

Documentation

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