IGB User's Guide
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New Features in IGB 6.7 

Welcome to IGB 6.7. We have made many changes and improvements to make IGB even easier to use.

Many changes, such as moving the Species and Genome Version to Current Sequences tab and the redesigned Bookmarks tab will be immediately obvious to IGB veterans, but there are many more new and exciting functions you should explore in IGB 6.7.

Major thanks are due to IGB software developer Hiral Vora, who led the effort and kept us all on track for the current release. Thank you Hiral!

Panels and tabs redesigned

To make IGB easier to use, we re-configured the user interface for several IGB tabs and panels including

  • Bookmarks tab
  • the Export File window
  • the Web Links Tools interface.

We also re-designed the IGB start screen.  Now, when you start IGB for the first time, you'll see a new start screen that provides quick and easy access to a variety of model organisms, helping new users jump right in.

Credit for this new interface go to Dr. Jeremy Villalobos and Graduate Research Assistant David Norris.

Better Bookmarks tab - and support for comments

The Bookmarks tab now supports adding comments to bookmarks and bookmark folders.

When you create a new bookmark, IGB will give you the option to add a free text comment. (As before, you can name bookmarks whatever you like or just use the IGB-supplied default.)

The Add Bookmark function offers the option of making one of two types of bookmarks:

  • a Position Only bookmark which records genomic location
  • or a Position and Data bookmark, which also records data sets currently being displayed

Returning to a Position Only bookmark returns you to the bookmarked genomic position but won't load data.

Returning to a Position and Data bookmark returns you to the bookmarked genomic position and also re-loads data sets that were in the original scene (provided they are available).

Right clicking a bookmark will open a new window displaying bookmark attributes. 

Thank you to Graduate Research Assistants Zhong Ren and David Norris for programming and also to Dr. Alyssa Gulledge for design and usability evaluation.

New options for exporting image files

Along with a redesign to improve ease of use, the Export interface also features new options not previously available. Users can now specify image size and file type for export. You can still specify which part of the IGB display you'd like to export, e.g, the main display image, the main image with the track labels, or the entire window with tabbed panels (such as Selection Info) showing. IGB can currently export images in PNG or JPEG formats.

We are also added a new feature that allows you to set image resolution/DPI. IGB now makes it easier to create high-quality images of 300 dpi or better (the minimum required for images destined for publication in printed journals).

Note to current users: Unfortunately, we had to remove export to PDF and other vector graphics formats. There were a number of show-stopping bugs in the external libraries we were using to support export in those formats. We are looking for new libraries that will be able to support those formats and hope to aim this functionality in the next release.

Thank you to Zhong Ren (CS Masters student) for programming the Export Image window.

Autoload for features that use sequence data

A number of IGB ffeatures that require access to sequence data, such as Restriction Site mapping, the Sequence Viewer for gene models and Search Residues functions. Previously, IGB would ask you before loading sequence data. Starting with IGB 6.7, IGB will automatically load sequence data from available IGB QuickLoad or DAS sites, speeding the process of retrieving information you need for analysis and visualization. However, you can still Load Sequence in View or Load All Sequence information from the Data Access panel.

Tip: You can control which server IGB will use for accessing sequence data by changing the ordering of Data Sources in the Data Sources Preferences tab. Data providers differ on whether it is better to deliver masked versus unmasked genomic sequence to users, and so we decided to give users the ability to control which data source provides the reference genome sequence. Thanks are due to developer Lance Frohman (Genentech) who added this feature.

Expanded residue Search function displays multiple sequences

With IGB 6.7, we have introduced the ability to overlay multiple sequence Search results (up to 7 different searches).

The basic Search Residue function hasn't changed; as before, you type in the sequence you are searching for and IGB returns a list of 'hits' and adds colored bars to the sequence indicating the location of matches.

However, if you check the new Overlay option, subsequent residue searches will be added to the list and highlighted in new colors without removing previous search results.

Use this new feature when you need to display multiple sequence features in the same view, such as forward and reverse primers for PCR primers, transcription factor binding sites, and so on. 

Thanks are due to Dr. Alyssa Gulledge for designing and testing this new feature.

This image shows the 3 primers needed for determining splice variant choice for the AT1G07940 gene of Arabidopsis thaliana, all shown in the same view.

Expanded file types and increased save options

We are always expanding our ability to support new file types. With IGB 6.7, we can now support BedDetail files and tabix indexed GFF files. If there is a file type we don't support yet, let us know! IGB has allowed users to save annotation tracks (including tracks created through Track Operations) as .bed files. Now, IGB can now save graph tracks (including tracks generated with IGB tools in the Graph Adjuster panel!) as .bedgraph files.

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