Frequently Asked Questions

What is the difference between WebGBrowse and GBrowse?

The Generic Genome Browser (GBrowse) is one of the most widely used visualization tool for displaying sequence features along a reference sequence. However, the installation and configuration of GBrowse can be tedious for many biologists who are not computer savvy or lack adequate computational resources. WebGBrowse can be considered as a web front-end for GBrowse, providing GBrowse functionality *without* the need for users to:

  • Prepare any computer hardware
  • Install any software
  • Learn the semantics involved in GBrowse configuration for feature display.

Instead, WebGBrowse allows users to simply upload the reference sequence and feature information (e.g., gene coordinates and tiling array results) in the standard GFF3 format. A well designed interface powered by a glyph library will assist the user in configuring the uploaded features for display in a step-by-step guided way and displaying with the GBrowse system that is pre-installed on our server. WebGBrowse also helps users keep track of their previous submissions via links provided in Email notifications.



Who may want to use WebGBrowse?

Most model organism databases have set up GBrowse to display the genome of interest for their research community. Increasingly however, such a centralized display strategy is not good enough to satisfy the diverse needs of researchers. With the rapid advent of sequencing technology, more and more individual biology laboratories are engaged in genome sequencing. The sequencing targets can be a particular species, strain, or specific regions of some individuals in a population (currently, such a trend is perhaps more prominent with microbiologists). However, individual researchers may find that centralized community databases are not always flexible to accommodate their specific visualization needs of genomic data (e.g., a new BAC sequenced in their labs) as well as the displayed features (e.g., their own tiling array experiment results). If you are one of such researchers and do not wish to go through the hassles of installing and configuring GBrowse, WebGBrowse is designed for you. Having said that, WebGBrowse can be used by anyone who wants to configure their GFF3 datasets for GBrowse display.



What software should I install on my computer to use WebGBrowse?

In order to use WebGBrowse, all you need is a compatible web browser and an internet connection. A spreadsheet software such as Microsoft Excel may be helpful in generating the tab-delimited GFF3 data.



How can I get started?

A step-by-step and well illustrated tutorial provided with a sample dataset to work with is a good starting point for a beginner. If you have a well formed GFF3 dataset, you can upload it at the WebGBrowse home page. The WebGBrowse configuration panel will help you through the rest of the configuration process.



What is GFF3 specification?

The GFF3 Specification is available on the Sequence Ontology website. It describes the format in which the annotation information can be presented in GFF3 standards. GBrowse recognizes data presented in this format and applies the configuration settings to visualize the individual features in the form of tracks in the GBrowse display.



Can I include any sequence information in my GFF3 file?

Yes, according to the GFF3 Sequence Section in the GFF3 specification "GFF3 files can also include sequence in FASTA format at the end of the file. The FASTA sequences are preceded by a ##FASTA line. This sequence section is optional. If present, the sequence section can define sequence for any landmark used in column 1 (the frame of reference)". The sample dataset (volvox.gff3) we provided illustrates the genome sequence included in the GFF3 file.



I am completely new to GBrowse. Are there any tutorials or resources which can help me learn and understand the various features available with GBrowse?

OpenHelix has recently released a very comprehensive GBrowse user tutorial which basically helps users to learn the various features available with GBrowse, such as basic layout of GBrowse, various search methods, access detailed annotation data, select and customize annotations using tracks and uploading and incorporating one's own data or other external data sources.



Can I still use the custom track submission function in GBrowse?

All the features of GBrowse including that of custom track submission will be available as usual with the GBrowse display. For more details on the features available with GBrowse, please refer to the GBrowse user tutorial from OpenHelix.



WebGBrowse doesnot display my data properly, why?

First, your input data must be in the standard GFF3 format (this is required by the underlying GBrowse system). Second, WebGBrowse generates a configuration file from the input GFF3 data file, based on user selected configuration values. If your gff file is of proper GFF3 format and you still face problems, please contact support.



Can I download the Configuration file that is generated by WebGBrowse?

Yes, you can download the configuration file that WebGBrowse generates by clicking the "Download Configuration" button from the WebGBrowse Control Panel available in the GBrowse display page. Please refer to the tutorial for more details.



Can I start the configuration process from a pre-created configuration file rather than from the scratch?

Yes, if you have a pre-created GBrowse configuration file, you can use it as a template by uploading it along with the GFF3 dataset in the WebGBrowse Input form on the home page. It is recommended to use only those configuration files which are generated from WebGBrowse. Once the dataset along with the configuration template are uploaded, the WebGBrowse Configuration Panel will display the pre-created tracks in the "Tracks Added" section. You can add further tracks if you wish or you can modify the existing tracks. Please refer to the tutorial for more details.



Can I apply the same configuration for multiple GFF3 datasets?

Yes, you can do that by downloading the configuration file from the GBrowse display of the first dataset and using it as a template for the remaining datasets. Also see the previous two questions.



I lost the email sent by WebGBrowse, how do I recover the URLs to my result page?

Currently the only way for you to recover your lost emails it to uplaad any gff3 file to WebGBrowse. The email which is sent back from WebGBrowse contains a link for you to view all your previously uploaded files. Unfortunately, there is no way for us to provide this in case you have not specified an email address or if you forgot the email address that you have used with WebGBrowse.



How can I obtain the source code of WebGBrowse?

You can download the source code from the Software page. You will also get the installation instructions.



How can I get help on WebGBrowse?

For help, please contact us at biohelp@cgb.indiana.edu



Page last updated by Ram Podicheti on March 11, 2009 04:25 PM EST

IU Copyright © The Trustees of Indiana University | Copyright Complaints