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Credit for this new interface go to Jeremy Villalobos (programming), and David Norris (programming), and Ann Loraine (design and image editing).
Better Bookmarks
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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
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, an which also records data sets currently being displayed. 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.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.
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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 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 even it 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 -- 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 InformationInfo) showing. You
IGB can export images as .png or .jpeg files and use these images for publications, slides, or sharing data with colleaguesin PNG or JPEG formats.
Thank you to Zhong Ren for programmign the Export Image window.
Autoload for features that use sequence data
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IGB has many features A number of IGB ffeatures that require laoding 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. Starging with IGB 6.7, IGB will automatically load sequence data, speeding the process of retrieving the 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.
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
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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 adds colored bars to the sequence bar indicating the exact location(s) using a color segmentlocation of matches. With the new Overlay option activated, subsequent residue searches will be added to the list and highlight highlighted 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!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.
This image shows the 3 primers needed for determining splice variant choice for the AT1G07940 gene of Arabidopsis thaliana, all overlayed into shown in the same imageview.
Expanded file types and increased save options
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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.