under construction
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.
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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!
Bookmarks, Export, Web Link and Start Screen are all 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.
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Credit for this new interface go to Jeremy Villalobos (programming), David Norris (programming), and Ann Loraine (design and image editing).
Better Bookmarks:
Bookmarks now support comments for each bookmark and for bookmark folders. This allows users to give bookmarks easy-to-remember names, but also allows users to make notes on what they see or even what lab the bookmarks were imported from. Add Bookmark still offers 2 options of Position Only which simple remembers the genomic location or a Position and Data bookmark, an 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 the properties window with a listing of the files that were loaded, as well as time/date created and genome version that was in use. In combination with the redesigned panel, users will find Bookmarks to be more helpful for visualizing, analyzing and sharing data than ever.
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, file type, and image resolution (DPI) for export. If you are using IG 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 even easier to create high-quality images of 300 dpi or better (the minimum required for images destined for publication in printed journals). You can still specify the type of image -- e.g, the main display image, the main image with the track labels, or the entire window with panels (such as Selection Information) showing. You can export images as .png or .jpeg files and use these images for publications, slides, or sharing data with colleagues.
Autoload for features that use sequence data.
IGB has many features that require laoding sequence data, such as Restriction Site mapping, Sequence Viewer for gene models and Search Residues. Previously, IGB would ask you before loading sequence data. Starging with IGB 6.7, IGB will automatically load sequence data, speeding the process of retrieving the 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.
New features for Main View:
We added several new features to the main view to improve the user experience. One new feature creates a track immediately after opening a file or accessing a data set under the Data Access panel, even before you load the data into the main view. This is where the data will appear once after clicking the Load Data button. Another feature to improve interaction with displayed data, is that the arrow cursor changes to a hand/pointer when your mouse passes over selectable features, indicating that you can interact with these items.
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 marks on the sequence bar the exact location(s) using a color segment. With the new Overlay option activated, subsequent residue searches will be added to the list and highlight in new colors, all at the same time. This is a powerful tool for many purposes! It can be used for showing multiple PCR primers in their accurate positions, aligned in the area of interest; it can show up to 7 enhancer, inhibitor or other elements in a promoter region, all in their accurate relationship to one another; the list goes on!
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This image shows the 3 primers needed for determining splice variant choice for the AT1G07940 gene of Arabidopsis thaliana, all overlayed into the same image.
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.