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 willl 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 the Bookmarks tab, the Export File window, and the Web Links Tools interface. Each of these new designs makes it easier to find information and perform functions. Veteran IGB users will also notice that menus and pop-up windows use new, more intuitive names for functions, making the IGB interface more consistent.
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 Jeremy Villalobos and David Norris.
Better Bookmarks
Bookmarks now support comments for each bookmark and for 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. The enhanced bookmark remembers and re-loads location AND data sets that were in the original scene (provided they are available). Right clicking on the Position and Data bookmark will open a new window displaying bookmark attributes, such as loaded data sets.
Thank you to Nick Ren and David Norris for programming and also to Alyssa Gulledge for assisting with 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 working on a PROTOTYPE feature to allow IGB to change the DPI/reolution of the image. If you are using IGB to make figures for publication in print journals, you'll need the ability to create high-quality, high-resolution images necessary for publication. 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). In conjunction with the resolution feature, we will also be adding in more file types, to allow users to create the image that they need.
Thank you to Zhong Ren 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, 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.
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; 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. With the new Overlay option activated, 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.