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 a redesign to improve ease of use, the Export interface also received new options. Users can set image size, file type, and image resolution (DPI) for export. 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). Users can still select whether the want the main image, the main image with the track labels, or the entire window with panels (such as Selection Information) showing. As .png or .jpeg files, these images can readily be used for journal article, presentations or just sharing data with others.
Autoload for features that use sequence data.
IGB has many features that require sequence data, such as Restriction Site mapping, Sequence Viewer for gene models and Search Residues. IGB now triggers automatic loading of sequence data, speeding the process of getting you the information you want. Users can still Load Sequence in View or Load All Sequence information from the Data Access panel.
New features for Main View:
We added several nice 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 residue search 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!
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.