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Credit for this new interface go to Dr. Jeremy Villalobos and Graduate Research Assistant David Norris.
Better Bookmarks
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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 as well as the 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 Graduate Research Assistants Zhong Ren and David Norris for programming and also to Dr. 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 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 added a PROTOTYPE new 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 publicationthat 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). 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.
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.
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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. With
However, if you check 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.
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