Tool
Annotation
Archived

ZMap

ZMap is a genome browser written in C++ with the aim of providing fast access to high volume data.

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.

Archive Page

This page is maintained as a historical record and is no longer being updated.

This page is now archived and is not being updated. It is being maintained as a historical record of the work carried out by the HAVANA team at the Wellcome Sanger Institute and the software is still available for download and use.

Further information

Supported platforms:

ZMap features

  • zoom
  • 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).

Getting Started:

Run zmap –help to see usage information. ZMap can be run with a GFF file on the command-line or with a configuration file that sets up the data sources. A sample GFF file is provided in the examples directory; 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.

ZMap is free software and is distributed under the terms of the Apache Version 2.0 License.

Please cite zmap by referring to the ZMap website

Contact

If you need help or have any queries, please contact us using the details below.

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

If you have a bug or feature request please raise a ticket by emailing zmap@sanger.ac.uk

For any other enquires please email the Annosoft team


Sanger Institute Contributors

Previous contributors

Photo of Gemma Guest

Gemma Guest

Former Senior Software Developer in the Annosoft Team

Photo of Dr Ed Griffiths

Dr Ed Griffiths

Former Senior Scientific Manager