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Custom Annotation
Mini module
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Overview

• KaryoView
• DAS
• URL-based upload

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KaryoView

• Display data in customisable single chromosome or
  entire karyotype ideograms
• Upload data using the KaryoView wizzard
• http//www.ensembl.org/Homo_sapiens/karyoview
• For more information see the online Help pages
• HELP gt Data Displays Ensembl KaryoView

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KaryoView
Examples
Location of caspase genes in human
Density of RNA genes along human chromosome 1
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DAS

• Display data in the Ensembl Genome browser
• (ContigView, CytoView, GeneView, ProtView)
• By uploading data into an internal DAS source
  within Ensembl
• For small datasets
• By attaching a new external DAS source
• For larger datasets
• Allows viewing of the data in other DAS clients
• Allows usage of the data by other applications

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DAS

• Distributed Annotation System
• Developed in 1999/2000 by Lincoln Stein (CSHL)
  and collaborators as a GFF-based web service.
• Biodas.org (http//www.biodas.org)
• A client-server system in which a single client
  integrates information from multiple servers.
• It allows a single machine to gather up genome
  annotation information from multiple distant
  websites, collate the information, and display it
  to the user in a single view.

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DAS
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DAS

• The annotations may be shared more easily
• The amount of data which needs to be stored
  locally is decreased
• Responsibility for updating and maintaining the
  data is left with the original data provider
• Annotation can be stored in a variety of formats
• Other programs, even other types of programs (not
  annotation viewers), may use the data

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DAS

• For more information on how to upload data to the
• Ensembl DAS server or how to set up your own
• DAS server
• See the online Help pages
• HELP gt Custom Annotation DasConfView
• Contact the Ensembl DAS team
• das_at_ebi.ac.uk

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URL-based Upload

• Display small datasets in the Ensembl Genome
  browser (ContigView, CytoView)
• Based on the custom annotation track system of
  the UCSC browser
• Allowed formats GFF, GTF, BED, PSL and WIG
• For more information see the online Help pages
• HELP gt Custom Annotation Upload your data -
  URL

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URL-based Upload
(1) Create an annotation file
Example of a file in GFF format
ltsequencegtltsourcegtltfeaturegtltstartgtltendgtltscoregtltstr
andgtltframegtltgroupgt
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URL-based Upload

• (2) Store your source file in a place where
  Ensembl can access it (e.g. your public_html
  folder)
• (3) Add your source to Ensembl by entering its
  URL on the Urlsource page
• ContigView gt DAS Sources gt URL based data

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URL-based Upload
Result
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Q

A
Q U E S T I O N S A N S W E R S