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

Supported platforms

  • Linux
  • Mac OS X (Intel)
  • Windows (under Cygwin)

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).

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 1.2.0, created on Fri Nov 28 09:47:15 GMT 2014:
seqtools-4.31.tar.gz
zmap-1.2.0.tar.gz

Development build

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

The latest version is 1.2.0-71-g262c6f6, created on Fri Nov 28 10:24:39 GMT 2014:
seqtools-4.31-21-ga4bb.tar.gz
zmap-1.2.0-71-g262c6f6.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 1.2.0-71-g262c6f6, created on Fri Nov 28 23:31:52 GMT 2014:
seqtools-4.31-21-ga4bb.tar.gz
zmap-1.2.0-71-g262c6f6.tar.gz

Installation

Linux

  • Install the following pre-requisites. This is most easily done using your system package manager (e.g. synaptic on Ubuntu, available from the System/Administration menu). Depending on your system, packages may be named differently or additional packages may be required. In this case the ./configure step below will fail and you will need to install the required package before running it again.
    libcurl4-gnutls-dev
    libgtk-2.0-dev
    libglib-2.0-dev
    libreadline6-dev
    libsqlite3-dev        (optional)
    
  • In the terminal, unpack the downloaded zmap tar file using the following command, where XXX is the version you downloaded:
    tar -xf zmap-XXX.tar.gz
    
  • To install in the default location (usually /usr/bin):
    cd zmap-XXX
    ./configure
    make
    make install
  • Optionally, repeat the process for SeqTools if you want the Blixem and Dotter programs to be available from within ZMap (these can be installed at a later date if you are not sure).
  • To install in a different location, or for help with dependencies, see the tips section. For more detailed instructions, see the INSTALL file in the source code.

Mac OS X

  • Install the following pre-requisites. We strongly recommend that you use MacPorts to install these packages as this will also install any dependencies for you.
    curl
    gtk2
    glib2
    readline
    sqlite3 (optional)
    
  • In the terminal, unpack the downloaded zmap tar file using the following commands, where XXX is the version you downloaded:
    tar -xf zmap-XXX.tar.gz
    
  • To install in the default location (usually /opt/local/bin):
    cd zmap-XXX
    ./configure
    make
    make install
    
  • Optionally, repeat the process for SeqTools if you want the Blixem and Dotter programs to be available from within ZMap (these can be installed at a later date if you are not sure).
  • To install in a different location, or for help with dependencies, see the tips section. For more detailed instructions, see the INSTALL file in the source code.

Windows

ZMap cannot currently run natively on Windows. However, it can be installed and run using Cygwin (which provides a Linux-like environment on Windows).

  • From the Cygwin website, download setup-x86.exe (or setup-x86_64.exe if you have a 64-bit machine).
  • Run the setup program, accepting all the default options. You will need to choose a mirror on the Choose Download Site page (e.g. cygwin.mirror.constant.com).
  • On the Select Packages page, select these packages:
    Devel/gcc-core
    Devel/gcc-g++
    Devel/libsqlite3-devel    (optional)
    Devel/make
    Devel/pkg-config
    Editors/nano              (optional)
    Libs/libcurl-devel
    Libs/libglib2.0-devel *** also tick the SOURCE checkbox ***
    Libs/libgtk2.0-devel  *** also tick the SOURCE checkbox ***
    Libs/libreadline-devel    (or Libs/readline)
    Web/wget                  (optional)
    X11/xinit
    
  • When installation is complete, open the Cygwin terminal and type the following commands, replacing XXX with the version of ZMap you want to download.
    wget ftp://ftp.sanger.ac.uk/pub/resources/software/zmap/PRODUCTION/zmap-XXX.tar.gz
    tar -xf zmap-XXX.tar.gz
    cd zmap-XXX
    ./configure
    make
    make install
    
  • Optionally, repeat the process for SeqTools if you want the Blixem and Dotter programs to be available from within ZMap (these can be installed at a later date if you are not sure).
  • Before you can run the programs, you will need to run the following commands:
    export DISPLAY=:0
    startxwin -- -emulate3buttons &
    To run these automatically each time Cygwin starts, edit the following file using the nano editor and paste the commands at the bottom:
    nano ~/.bash_profile
    
  • For further help, see the tips section or the INSTALL file in the source code.

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
    
  • If GTK+ is not in the default location then you may need to pass its location to the configure script. GTK+ is usually installed in /usr/lib, /usr/local/lib, /opt/lib or /opt/local/lib. If GTK+ is in e.g. /opt/local/lib then you would call configure with the following arguments:
    ./configure PKG_CONFIG_PATH=/opt/local/lib/pkgconfig LDFLAGS="-Xlinker -rpath -Xlinker /opt/local/lib"
    

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/aqo3wpoi