New Features in IGB 6.7
Welcome to IGB 6.7! We have made many changes and improvements to make IGB even easier for users! Many changes, such as moving the Species and Genome Version to Current Sequences tab and the redesigned Bookmarks tab are obvious, but there are many more new and exciting functions you should explore!
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. Finally, the new start screen gives quick and easy access to a variety of model organisms, helping new users jump right in!
Improved 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!
Added Export options:
Along with the interface redesign, the Export interface now allows users to set image size, type, and image resolution (DPI). 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.
Autoload for features that use sequence data.
IGB features that require sequence data, such as Restriction Site mapping and Search Residues, now trigger automatic loading of sequence data, which includes a graphic to show the download progress. Users can still load sequence information from the Data Access panel for visualization.
New features for Main View:
We added several nice features to the main view to improve usability. First off, you will see when you start IGB, the welcome screen now has shortcuts for commonly used genomes – one click on a shortcut picture takes you to the most up-to-date genome version for the selected species. Another new feature improves IGB's data loading; now, when you open a file or click a data set under the Data Access panel, a new track for that data set will appear immediately, showing you where the data will appear once you've loaded it by clicking the "Load Data" button. And to help you interact with displayed data and other elements of the IGB graphical interface, the arrow cursor changes to a hand/pointer when your mouse passes over selectable features, indicating that you can select or otherwise interact with these items.
Expanded residue Search function displays multiple sequences:
We introduced the ability to show multiple sequence search results (up to 7 different searches) all aligned onto the genome. The basic residue search function hasn't changed, but if you click the new 'overlay' option while doing a second residue search, IGB will draw results from the second search in a different color and display them alongside results from previous searches. This is useful for showing both primers of a PCR primer pair, for example, or for showing up to 7 elements in a promoter region, and so on. A very handy tool!
Support for new file types:
We are always expanding our ability to support new file types. With IGB 6.7, we can now support BedDetail files [http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7] and tabix indexed GFF files [http://www.ncbi.nlm.nih.gov/pubmed/21208982]. If there is a file type we don't support yet, let us know! Additionally IGB can now SAVE graph files (including graph files generated with IGB tools!) as .bedgraph files.